23 files changed, 464 insertions, 107 deletions
diff --git a/klm/util/exception.cc b/klm/util/exception.cc
index 557c3986..083bac20 100644
--- a/klm/util/exception.cc
+++ b/klm/util/exception.cc
@@ -51,6 +51,11 @@ void Exception::SetLocation(const char *file, unsigned int line, const char *fun
 }
 
 namespace {
+// At least one of these functions will not be called.
+#ifdef __clang__
+#pragma clang diagnostic push
+#pragma clang diagnostic ignored "-Wunused-function"
+#endif
 // The XOPEN version.
 const char *HandleStrerror(int ret, const char *buf) {
   if (!ret) return buf;
@@ -61,6 +66,9 @@ const char *HandleStrerror(int ret, const char *buf) {
 const char *HandleStrerror(const char *ret, const char * /*buf*/) {
   return ret;
 }
+#ifdef __clang__
+#pragma clang diagnostic pop
+#endif
 } // namespace
 
 ErrnoException::ErrnoException() throw() : errno_(errno) {
diff --git a/klm/util/exception.hh b/klm/util/exception.hh
index 74046cf9..0298272b 100644
--- a/klm/util/exception.hh
+++ b/klm/util/exception.hh
@@ -98,6 +98,9 @@ template <class Except, class Data> typename Except::template ExceptionTag<Excep
 #define UTIL_THROW_IF(Condition, Exception, Modify) \
   UTIL_THROW_IF_ARG(Condition, Exception, , Modify)
 
+#define UTIL_THROW_IF2(Condition, Modify) \
+  UTIL_THROW_IF_ARG(Condition, util::Exception, , Modify)
+
 // Exception that records errno and adds it to the message.
 class ErrnoException : public Exception {
   public:
@@ -111,6 +114,13 @@ class ErrnoException : public Exception {
     int errno_;
 };
 
+// file wasn't there, or couldn't be open for some reason
+class FileOpenException : public Exception {
+  public:
+	FileOpenException() throw() {}
+    ~FileOpenException() throw() {}
+};
+
 // Utilities for overflow checking.  
 class OverflowException : public Exception {
   public:
diff --git a/klm/util/file.cc b/klm/util/file.cc
index bef04cb1..51eaf972 100644
--- a/klm/util/file.cc
+++ b/klm/util/file.cc
@@ -17,7 +17,11 @@
 #include <fcntl.h>
 #include <stdint.h>
 
-#if defined(_WIN32) || defined(_WIN64)
+#if defined __MINGW32__
+#include <windows.h>
+#include <unistd.h>
+#warning "The file functions on MinGW have not been tested for file sizes above 2^31 - 1.  Please read https://stackoverflow.com/questions/12539488/determine-64-bit-file-size-in-c-on-mingw-32-bit and fix"
+#elif defined(_WIN32) || defined(_WIN64)
 #include <windows.h>
 #include <io.h>
 #include <algorithm>
@@ -76,7 +80,13 @@ int CreateOrThrow(const char *name) {
 }
 
 uint64_t SizeFile(int fd) {
-#if defined(_WIN32) || defined(_WIN64)
+#if defined __MINGW32__
+  struct stat sb;
+  // Does this handle 64-bit?
+  int ret = fstat(fd, &sb);
+  if (ret == -1 || (!sb.st_size && !S_ISREG(sb.st_mode))) return kBadSize;
+  return sb.st_size;
+#elif defined(_WIN32) || defined(_WIN64)
   __int64 ret = _filelengthi64(fd);
   return (ret == -1) ? kBadSize : ret;
 #else // Not windows.
@@ -100,7 +110,10 @@ uint64_t SizeOrThrow(int fd) {
 }
 
 void ResizeOrThrow(int fd, uint64_t to) {
-#if defined(_WIN32) || defined(_WIN64)
+#if defined __MINGW32__
+    // Does this handle 64-bit?  
+    int ret = ftruncate
+#elif defined(_WIN32) || defined(_WIN64)
     errno_t ret = _chsize_s
 #elif defined(OS_ANDROID)
     int ret = ftruncate64
@@ -115,7 +128,7 @@ namespace {
 std::size_t GuardLarge(std::size_t size) {
   // The following operating systems have broken read/write/pread/pwrite that
   // only supports up to 2^31.
-#if defined(_WIN32) || defined(_WIN64) || defined(__APPLE__) || defined(OS_ANDROID)
+#if defined(_WIN32) || defined(_WIN64) || defined(__APPLE__) || defined(OS_ANDROID) || defined(__MINGW32__)
   return std::min(static_cast<std::size_t>(static_cast<unsigned>(-1)), size);
 #else
   return size;
@@ -251,7 +264,10 @@ typedef CheckOffT<sizeof(off_t)>::True IgnoredType;
 // Can't we all just get along?
 void InternalSeek(int fd, int64_t off, int whence) {
   if (
-#if defined(_WIN32) || defined(_WIN64)
+#if defined __MINGW32__
+    // Does this handle 64-bit?
+    (off_t)-1 == lseek(fd, off, whence)
+#elif defined(_WIN32) || defined(_WIN64)
     (__int64)-1 == _lseeki64(fd, off, whence)
 #elif defined(OS_ANDROID)
     (off64_t)-1 == lseek64(fd, off, whence)
diff --git a/klm/util/file_piece.cc b/klm/util/file_piece.cc
index b5961bea..9c7e00c4 100644
--- a/klm/util/file_piece.cc
+++ b/klm/util/file_piece.cc
@@ -74,7 +74,9 @@ StringPiece FilePiece::ReadLine(char delim) {
       }
     }
     if (at_end_) {
-      if (position_ == position_end_) Shift();
+      if (position_ == position_end_) {
+        Shift();
+      }
       return Consume(position_end_);
     }
     skip = position_end_ - position_;
diff --git a/klm/util/file_piece.hh b/klm/util/file_piece.hh
index c07c6011..ed3dc5ad 100644
--- a/klm/util/file_piece.hh
+++ b/klm/util/file_piece.hh
@@ -12,6 +12,7 @@
 #include <iosfwd>
 #include <string>
 
+#include <assert.h>
 #include <stdint.h>
 
 namespace util {
@@ -66,8 +67,14 @@ class FilePiece {
 
     // Skip spaces defined by isspace.
     void SkipSpaces(const bool *delim = kSpaces) {
+      assert(position_ <= position_end_);
       for (; ; ++position_) {
-        if (position_ == position_end_) Shift();
+        if (position_ == position_end_) {
+          Shift();
+          // And break out at end of file.
+          if (position_ == position_end_) return;
+        }
+        assert(position_ < position_end_);
         if (!delim[static_cast<unsigned char>(*position_)]) return;
       }
     }
@@ -86,6 +93,7 @@ class FilePiece {
     template <class T> T ReadNumber();
 
     StringPiece Consume(const char *to) {
+      assert(to >= position_);
       StringPiece ret(position_, to - position_);
       position_ = to;
       return ret;
diff --git a/klm/util/file_piece_test.cc b/klm/util/file_piece_test.cc
index 7336007d..4361877f 100644
--- a/klm/util/file_piece_test.cc
+++ b/klm/util/file_piece_test.cc
@@ -1,4 +1,4 @@
-// Tests might fail if you have creative characters in your path.  Sue me.  
+// Tests might fail if you have creative characters in your path.  Sue me.
 #include "util/file_piece.hh"
 
 #include "util/file.hh"
@@ -55,7 +55,7 @@ BOOST_AUTO_TEST_CASE(MMapReadLine) {
 
 #if !defined(_WIN32) && !defined(_WIN64) && !defined(__APPLE__)
 /* Apple isn't happy with the popen, fileno, dup.  And I don't want to
- * reimplement popen.  This is an issue with the test.  
+ * reimplement popen.  This is an issue with the test.
  */
 /* read() implementation */
 BOOST_AUTO_TEST_CASE(StreamReadLine) {
@@ -67,7 +67,7 @@ BOOST_AUTO_TEST_CASE(StreamReadLine) {
 
   FILE *catter = popen(popen_args.c_str(), "r");
   BOOST_REQUIRE(catter);
-  
+
   FilePiece test(dup(fileno(catter)), "file_piece.cc", NULL, 1);
   std::string ref_line;
   while (getline(ref, ref_line)) {
@@ -107,8 +107,8 @@ BOOST_AUTO_TEST_CASE(PlainZipReadLine) {
 }
 
 // gzip stream.  Apple doesn't like popen, fileno, dup.  This is an issue with
-// the test.  
-#ifndef __APPLE__
+// the test.
+#if !defined __APPLE__ && !defined __MINGW32__
 BOOST_AUTO_TEST_CASE(StreamZipReadLine) {
   std::fstream ref(FileLocation().c_str(), std::ios::in);
 
@@ -117,7 +117,7 @@ BOOST_AUTO_TEST_CASE(StreamZipReadLine) {
 
   FILE * catter = popen(command.c_str(), "r");
   BOOST_REQUIRE(catter);
-  
+
   FilePiece test(dup(fileno(catter)), "file_piece.cc.gz", NULL, 1);
   std::string ref_line;
   while (getline(ref, ref_line)) {
diff --git a/klm/util/joint_sort.hh b/klm/util/joint_sort.hh
index 1b43ddcf..13a52b67 100644
--- a/klm/util/joint_sort.hh
+++ b/klm/util/joint_sort.hh
@@ -9,7 +9,6 @@
 
 #include <algorithm>
 #include <functional>
-#include <iostream>
 
 namespace util {
 
@@ -35,9 +34,10 @@ template <class KeyIter, class ValueIter> class JointIter {
       return *this;
     }
 
-    void swap(const JointIter &other) {
-      std::swap(key_, other.key_);
-      std::swap(value_, other.value_);
+    friend void swap(JointIter &first, JointIter &second) {
+      using std::swap;
+      swap(first.key_, second.key_);
+      swap(first.value_, second.value_);
     }
 
   private:
@@ -83,9 +83,11 @@ template <class KeyIter, class ValueIter> class JointProxy {
       return *(inner_.key_);
     }
 
-    void swap(JointProxy<KeyIter, ValueIter> &other) {
-      std::swap(*inner_.key_, *other.inner_.key_);
-      std::swap(*inner_.value_, *other.inner_.value_);
+    friend void swap(JointProxy<KeyIter, ValueIter> first, JointProxy<KeyIter, ValueIter> second) {
+      // Allow argument-dependent lookup.
+      using std::swap;
+      swap(*first.inner_.key_, *second.inner_.key_);
+      swap(*first.inner_.value_, *second.inner_.value_);
     }
 
   private:
@@ -138,14 +140,4 @@ template <class KeyIter, class ValueIter> void JointSort(const KeyIter &key_begi
 
 } // namespace util
 
-namespace std {
-template <class KeyIter, class ValueIter> void swap(util::detail::JointIter<KeyIter, ValueIter> &left, util::detail::JointIter<KeyIter, ValueIter> &right) {
-  left.swap(right);
-}
-
-template <class KeyIter, class ValueIter> void swap(util::detail::JointProxy<KeyIter, ValueIter> &left, util::detail::JointProxy<KeyIter, ValueIter> &right) {
-  left.swap(right);
-}
-} // namespace std
-
 #endif // UTIL_JOINT_SORT__
diff --git a/klm/util/mmap.cc b/klm/util/mmap.cc
index 6f79f26f..cee6a970 100644
--- a/klm/util/mmap.cc
+++ b/klm/util/mmap.cc
@@ -90,7 +90,9 @@ void scoped_memory::call_realloc(std::size_t size) {
   if (!new_data) {
     reset();
   } else {
-    reset(new_data, size, MALLOC_ALLOCATED);
+    data_ = new_data;
+    size_ = size;
+    source_ = MALLOC_ALLOCATED;
   }
 }
 
diff --git a/klm/util/multi_intersection.hh b/klm/util/multi_intersection.hh
index 8334d39d..04678352 100644
--- a/klm/util/multi_intersection.hh
+++ b/klm/util/multi_intersection.hh
@@ -66,7 +66,7 @@ template <class Iterator, class Output, class Less> void AllIntersection(std::ve
 
   std::sort(sets.begin(), sets.end(), detail::RangeLessBySize<boost::iterator_range<Iterator> >());
   boost::optional<Value> ret;
-  for (boost::optional<Value> ret; ret = detail::FirstIntersectionSorted(sets, less); sets.front().advance_begin(1)) {
+  for (boost::optional<Value> ret; (ret = detail::FirstIntersectionSorted(sets, less)); sets.front().advance_begin(1)) {
     out(*ret);
   }
 }
diff --git a/klm/util/murmur_hash.cc b/klm/util/murmur_hash.cc
index 4f519312..189668c0 100644
--- a/klm/util/murmur_hash.cc
+++ b/klm/util/murmur_hash.cc
@@ -153,12 +153,19 @@ uint64_t MurmurHash64B ( const void * key, std::size_t len, uint64_t seed )
 
 // Trick to test for 64-bit architecture at compile time.  
 namespace {
+#ifdef __clang__
+#pragma clang diagnostic push
+#pragma clang diagnostic ignored "-Wunused-function"
+#endif
 template <unsigned L> inline uint64_t MurmurHashNativeBackend(const void * key, std::size_t len, uint64_t seed) {
   return MurmurHash64A(key, len, seed);
 }
 template <> inline uint64_t MurmurHashNativeBackend<4>(const void * key, std::size_t len, uint64_t seed) {
   return MurmurHash64B(key, len, seed);
 }
+#ifdef __clang__
+#pragma clang diagnostic pop
+#endif
 } // namespace
 
 uint64_t MurmurHashNative(const void * key, std::size_t len, uint64_t seed) {
diff --git a/klm/util/murmur_hash.hh b/klm/util/murmur_hash.hh
index ae7e88de..4891833e 100644
--- a/klm/util/murmur_hash.hh
+++ b/klm/util/murmur_hash.hh
@@ -5,8 +5,12 @@
 
 namespace util {
 
+// 64-bit machine version
 uint64_t MurmurHash64A(const void * key, std::size_t len, uint64_t seed = 0);
+// 32-bit machine version (not the same function as above)
 uint64_t MurmurHash64B(const void * key, std::size_t len, uint64_t seed = 0);
+// Use the version for this arch.  Because the values differ across
+// architectures, really only use it for in-memory structures.
 uint64_t MurmurHashNative(const void * key, std::size_t len, uint64_t seed = 0);
 
 } // namespace util
diff --git a/klm/util/pcqueue.hh b/klm/util/pcqueue.hh
index 3df8749b..07e4146f 100644
--- a/klm/util/pcqueue.hh
+++ b/klm/util/pcqueue.hh
@@ -1,6 +1,8 @@
 #ifndef UTIL_PCQUEUE__
 #define UTIL_PCQUEUE__
 
+#include "util/exception.hh"
+
 #include <boost/interprocess/sync/interprocess_semaphore.hpp>
 #include <boost/scoped_array.hpp>
 #include <boost/thread/mutex.hpp>
@@ -8,20 +10,68 @@
 
 #include <errno.h>
 
+#ifdef __APPLE__
+#include <mach/semaphore.h>
+#include <mach/task.h>
+#include <mach/mach_traps.h>
+#include <mach/mach.h>
+#endif // __APPLE__
+
 namespace util {
 
-inline void WaitSemaphore (boost::interprocess::interprocess_semaphore &on) {
+/* OS X Maverick and Boost interprocess were doing "Function not implemented."
+ * So this is my own wrapper around the mach kernel APIs.
+ */
+#ifdef __APPLE__
+
+#define MACH_CALL(call) UTIL_THROW_IF(KERN_SUCCESS != (call), Exception, "Mach call failure")
+
+class Semaphore {
+  public:
+    explicit Semaphore(int value) : task_(mach_task_self()) {
+      MACH_CALL(semaphore_create(task_, &back_, SYNC_POLICY_FIFO, value));
+    }
+
+    ~Semaphore() {
+      MACH_CALL(semaphore_destroy(task_, back_));
+    }
+
+    void wait() {
+      MACH_CALL(semaphore_wait(back_));
+    }
+
+    void post() {
+      MACH_CALL(semaphore_signal(back_));
+    }
+
+  private:
+    semaphore_t back_;
+    task_t task_;
+};
+
+inline void WaitSemaphore(Semaphore &semaphore) {
+  semaphore.wait();
+}
+
+#else
+typedef boost::interprocess::interprocess_semaphore Semaphore;
+
+inline void WaitSemaphore (Semaphore &on) {
   while (1) {
     try {
       on.wait();
       break;
     }
     catch (boost::interprocess::interprocess_exception &e) {
-      if (e.get_native_error() != EINTR) throw;
+      if (e.get_native_error() != EINTR) {
+        throw;
+      }
     }
   }
 }
 
+#endif // __APPLE__
+
 /* Producer consumer queue safe for multiple producers and multiple consumers.
  * T must be default constructable and have operator=.  
  * The value is copied twice for Consume(T &out) or three times for Consume(),
@@ -82,9 +132,9 @@ template <class T> class PCQueue : boost::noncopyable {
    
  private:
   // Number of empty spaces in storage_.
-  boost::interprocess::interprocess_semaphore empty_;
+  Semaphore empty_;
   // Number of occupied spaces in storage_.
-  boost::interprocess::interprocess_semaphore used_;
+  Semaphore used_;
 
   boost::scoped_array<T> storage_;
 
diff --git a/klm/util/pcqueue_test.cc b/klm/util/pcqueue_test.cc
new file mode 100644
index 00000000..22ed2c6f
--- /dev/null
+++ b/klm/util/pcqueue_test.cc
@@ -0,0 +1,20 @@
+#include "util/pcqueue.hh"
+
+#define BOOST_TEST_MODULE PCQueueTest
+#include <boost/test/unit_test.hpp>
+
+namespace util {
+namespace {
+
+BOOST_AUTO_TEST_CASE(SingleThread) {
+  PCQueue<int> queue(10);
+  for (int i = 0; i < 10; ++i) {
+    queue.Produce(i);
+  }
+  for (int i = 0; i < 10; ++i) {
+    BOOST_CHECK_EQUAL(i, queue.Consume());
+  }
+}
+
+}
+} // namespace util
diff --git a/klm/util/pool.cc b/klm/util/pool.cc
index db72a8ec..429ba158 100644
--- a/klm/util/pool.cc
+++ b/klm/util/pool.cc
@@ -25,9 +25,7 @@ void Pool::FreeAll() {
 }
 
 void *Pool::More(std::size_t size) {
-  // Double until we hit 2^21 (2 MB).  Then grow in 2 MB blocks. 
-  std::size_t desired_size = static_cast<size_t>(32) << std::min(static_cast<std::size_t>(16), free_list_.size());
-  std::size_t amount = std::max(desired_size, size);
+  std::size_t amount = std::max(static_cast<size_t>(32) << free_list_.size(), size);
   uint8_t *ret = static_cast<uint8_t*>(MallocOrThrow(amount));
   free_list_.push_back(ret);
   current_ = ret + size;
diff --git a/klm/util/probing_hash_table.hh b/klm/util/probing_hash_table.hh
index 51a2944d..38524806 100644
--- a/klm/util/probing_hash_table.hh
+++ b/klm/util/probing_hash_table.hh
@@ -2,6 +2,7 @@
 #define UTIL_PROBING_HASH_TABLE__
 
 #include "util/exception.hh"
+#include "util/scoped.hh"
 
 #include <algorithm>
 #include <cstddef>
@@ -25,6 +26,8 @@ struct IdentityHash {
   template <class T> T operator()(T arg) const { return arg; }
 };
 
+template <class EntryT, class HashT, class EqualT> class AutoProbing;
+
 /* Non-standard hash table
  * Buckets must be set at the beginning and must be greater than maximum number
  * of elements, else it throws ProbingSizeException.
@@ -33,7 +36,6 @@ struct IdentityHash {
  * Uses linear probing to find value.
  * Only insert and lookup operations.  
  */
-
 template <class EntryT, class HashT, class EqualT = std::equal_to<typename EntryT::Key> > class ProbingHashTable {
   public:
     typedef EntryT Entry;
@@ -43,7 +45,6 @@ template <class EntryT, class HashT, class EqualT = std::equal_to<typename Entry
     typedef HashT Hash;
     typedef EqualT Equal;
 
-  public:
     static uint64_t Size(uint64_t entries, float multiplier) {
       uint64_t buckets = std::max(entries + 1, static_cast<uint64_t>(multiplier * static_cast<float>(entries)));
       return buckets * sizeof(Entry);
@@ -69,6 +70,11 @@ template <class EntryT, class HashT, class EqualT = std::equal_to<typename Entry
 #endif
     {}
 
+    void Relocate(void *new_base) {
+      begin_ = reinterpret_cast<MutableIterator>(new_base);
+      end_ = begin_ + buckets_;
+    }
+
     template <class T> MutableIterator Insert(const T &t) {
 #ifdef DEBUG
       assert(initialized_);
@@ -82,7 +88,7 @@ template <class EntryT, class HashT, class EqualT = std::equal_to<typename Entry
 #ifdef DEBUG
       assert(initialized_);
 #endif
-      for (MutableIterator i(begin_ + (hash_(t.GetKey()) % buckets_));;) {
+      for (MutableIterator i = Ideal(t);;) {
         Key got(i->GetKey());
         if (equal_(got, t.GetKey())) { out = i; return true; }
         if (equal_(got, invalid_)) {
@@ -97,8 +103,6 @@ template <class EntryT, class HashT, class EqualT = std::equal_to<typename Entry
 
     void FinishedInserting() {}
 
-    void LoadedBinary() {}
-
     // Don't change anything related to GetKey,  
     template <class Key> bool UnsafeMutableFind(const Key key, MutableIterator &out) {
 #ifdef DEBUG
@@ -224,6 +228,8 @@ template <class EntryT, class HashT, class EqualT = std::equal_to<typename Entry
     }
 
   private:
+    friend class AutoProbing<Entry, Hash, Equal>;
+
     template <class T> MutableIterator Ideal(const T &t) {
       return begin_ + (hash_(t.GetKey()) % buckets_);
     }
@@ -247,6 +253,74 @@ template <class EntryT, class HashT, class EqualT = std::equal_to<typename Entry
 #endif
 };
 
+// Resizable linear probing hash table.  This owns the memory.  
+template <class EntryT, class HashT, class EqualT = std::equal_to<typename EntryT::Key> > class AutoProbing {
+  private:
+    typedef ProbingHashTable<EntryT, HashT, EqualT> Backend;
+  public:
+    typedef EntryT Entry;
+    typedef typename Entry::Key Key;
+    typedef const Entry *ConstIterator;
+    typedef Entry *MutableIterator;
+    typedef HashT Hash;
+    typedef EqualT Equal;
+
+    AutoProbing(std::size_t initial_size = 10, const Key &invalid = Key(), const Hash &hash_func = Hash(), const Equal &equal_func = Equal()) :
+      allocated_(Backend::Size(initial_size, 1.5)), mem_(util::MallocOrThrow(allocated_)), backend_(mem_.get(), allocated_, invalid, hash_func, equal_func) {
+      threshold_ = initial_size * 1.2;
+    }
+
+    // Assumes that the key is unique.  Multiple insertions won't cause a failure, just inconsistent lookup.
+    template <class T> MutableIterator Insert(const T &t) {
+      DoubleIfNeeded();
+      return backend_.UncheckedInsert(t);
+    }
+
+    template <class T> bool FindOrInsert(const T &t, MutableIterator &out) {
+      DoubleIfNeeded();
+      return backend_.FindOrInsert(t, out);
+    }
+
+    template <class Key> bool UnsafeMutableFind(const Key key, MutableIterator &out) {
+      return backend_.UnsafeMutableFind(key, out);
+    }
+
+    template <class Key> MutableIterator UnsafeMutableMustFind(const Key key) {
+      return backend_.UnsafeMutableMustFind(key);
+    }
+
+    template <class Key> bool Find(const Key key, ConstIterator &out) const {
+      return backend_.Find(key, out);
+    }
+
+    template <class Key> ConstIterator MustFind(const Key key) const {
+      return backend_.MustFind(key);
+    }
+
+    std::size_t Size() const {
+      return backend_.SizeNoSerialization();
+    }
+
+    void Clear() {
+      backend_.Clear();
+    }
+
+  private:
+    void DoubleIfNeeded() {
+      if (Size() < threshold_)
+        return;
+      mem_.call_realloc(backend_.DoubleTo());
+      allocated_ = backend_.DoubleTo();
+      backend_.Double(mem_.get());
+      threshold_ *= 2;
+    }
+
+    std::size_t allocated_;
+    util::scoped_malloc mem_;
+    Backend backend_;
+    std::size_t threshold_;
+};
+
 } // namespace util
 
 #endif // UTIL_PROBING_HASH_TABLE__
diff --git a/klm/util/proxy_iterator.hh b/klm/util/proxy_iterator.hh
index 0ee1716f..a2810a47 100644
--- a/klm/util/proxy_iterator.hh
+++ b/klm/util/proxy_iterator.hh
@@ -38,8 +38,8 @@ template <class Proxy> class ProxyIterator {
     typedef std::random_access_iterator_tag iterator_category;
     typedef typename Proxy::value_type value_type;
     typedef std::ptrdiff_t difference_type;
-    typedef Proxy & reference;
-    typedef Proxy * pointer;
+    typedef Proxy reference;
+    typedef ProxyIterator<Proxy> * pointer;
 
     ProxyIterator() {}
 
@@ -47,10 +47,10 @@ template <class Proxy> class ProxyIterator {
     template <class AlternateProxy> ProxyIterator(const ProxyIterator<AlternateProxy> &in) : p_(*in) {}
     explicit ProxyIterator(const Proxy &p) : p_(p) {}
 
-    // p_'s swap does value swapping, but here we want iterator swapping
+/*    // p_'s swap does value swapping, but here we want iterator swapping
     friend inline void swap(ProxyIterator<Proxy> &first, ProxyIterator<Proxy> &second) {
       swap(first.I(), second.I());
-    }
+    }*/
 
     // p_'s operator= does value copying, but here we want iterator copying.
     S &operator=(const S &other) {
@@ -77,8 +77,8 @@ template <class Proxy> class ProxyIterator {
 
     std::ptrdiff_t operator-(const S &other) const { return I() - other.I(); }
 
-    Proxy &operator*() { return p_; }
-    const Proxy &operator*() const { return p_; }
+    Proxy operator*() { return p_; }
+    const Proxy operator*() const { return p_; }
     Proxy *operator->() { return &p_; }
     const Proxy *operator->() const { return &p_; }
     Proxy operator[](std::ptrdiff_t amount) const { return *(*this + amount); }
diff --git a/klm/util/read_compressed_test.cc b/klm/util/read_compressed_test.cc
index 9cb4a4b9..50450a02 100644
--- a/klm/util/read_compressed_test.cc
+++ b/klm/util/read_compressed_test.cc
@@ -12,6 +12,23 @@
 
 #include <stdlib.h>
 
+#if defined __MINGW32__
+#include <time.h>
+#include <fcntl.h>
+
+#if !defined mkstemp
+// TODO insecure
+int mkstemp(char * stemplate)
+{
+    char *filename = mktemp(stemplate);
+    if (filename == NULL)
+        return -1;
+    return open(filename, O_RDWR | O_CREAT, 0600);
+}
+#endif
+
+#endif // defined
+
 namespace util {
 namespace {
 
diff --git a/klm/util/sized_iterator.hh b/klm/util/sized_iterator.hh
index dce8f229..a72657b5 100644
--- a/klm/util/sized_iterator.hh
+++ b/klm/util/sized_iterator.hh
@@ -36,7 +36,7 @@ class SizedInnerIterator {
     void *Data() { return ptr_; }
     std::size_t EntrySize() const { return size_; }
 
-    friend inline void swap(SizedInnerIterator &first, SizedInnerIterator &second) {
+    friend void swap(SizedInnerIterator &first, SizedInnerIterator &second) {
       std::swap(first.ptr_, second.ptr_);
       std::swap(first.size_, second.size_);
     }
@@ -69,17 +69,7 @@ class SizedProxy {
     const void *Data() const { return inner_.Data(); }
     void *Data() { return inner_.Data(); }
 
-  /**
-     // TODO: this (deep) swap was recently added. why? if any std heap sort etc
-     // algs are using swap, that's going to be worse performance than using
-     // =. i'm not sure why we *want* a deep swap. if C++11 compilers are
-     // choosing between move constructor and swap, then we'd better implement a
-     // (deep) move constructor. it may also be that this is moot since i made
-     // ProxyIterator a reference and added a shallow ProxyIterator swap? (I
-     // need Ken or someone competent to judge whether that's correct also. -
-     // let me know at graehl@gmail.com
-  */
-    friend void swap(SizedProxy &first, SizedProxy &second) {
+    friend void swap(SizedProxy first, SizedProxy second) {
       std::swap_ranges(
           static_cast<char*>(first.inner_.Data()),
           static_cast<char*>(first.inner_.Data()) + first.inner_.EntrySize(),
diff --git a/klm/util/sized_iterator_test.cc b/klm/util/sized_iterator_test.cc
new file mode 100644
index 00000000..c36bcb2d
--- /dev/null
+++ b/klm/util/sized_iterator_test.cc
@@ -0,0 +1,16 @@
+#include "util/sized_iterator.hh"
+
+#define BOOST_TEST_MODULE SizedIteratorTest
+#include <boost/test/unit_test.hpp>
+
+namespace util { namespace {
+
+BOOST_AUTO_TEST_CASE(swap_works) {
+  char str[2] = { 0, 1 };
+  SizedProxy first(str, 1), second(str + 1, 1);
+  swap(first, second);
+  BOOST_CHECK_EQUAL(1, str[0]);
+  BOOST_CHECK_EQUAL(0, str[1]);
+}
+
+}} // namespace anonymous util
diff --git a/klm/util/string_piece.hh b/klm/util/string_piece.hh
index 9cf4c7f6..84431db1 100644
--- a/klm/util/string_piece.hh
+++ b/klm/util/string_piece.hh
@@ -74,6 +74,12 @@ inline bool operator!=(const StringPiece& x, const StringPiece& y) {
 #endif // old version of ICU
 
 U_NAMESPACE_BEGIN
+
+inline bool starts_with(const StringPiece& longer, const StringPiece& prefix) {
+  int longersize = longer.size(), prefixsize = prefix.size();
+  return longersize >= prefixsize && std::memcmp(longer.data(), prefix.data(), prefixsize) == 0;
+}
+
 #else
 
 #include <algorithm>
@@ -212,7 +218,7 @@ class StringPiece {
   StringPiece substr(size_type pos, size_type n = npos) const;
 
   static int wordmemcmp(const char* p, const char* p2, size_type N) {
-    return memcmp(p, p2, N);
+    return std::memcmp(p, p2, N);
   }
 };
 
@@ -227,6 +233,10 @@ inline bool operator!=(const StringPiece& x, const StringPiece& y) {
   return !(x == y);
 }
 
+inline bool starts_with(const StringPiece& longer, const StringPiece& prefix) {
+  return longer.starts_with(prefix);
+}
+
 #endif // HAVE_ICU undefined
 
 inline bool operator<(const StringPiece& x, const StringPiece& y) {
diff --git a/klm/util/tokenize_piece.hh b/klm/util/tokenize_piece.hh
index a588c3fc..24eae8fb 100644
--- a/klm/util/tokenize_piece.hh
+++ b/klm/util/tokenize_piece.hh
@@ -58,6 +58,23 @@ class AnyCharacter {
     StringPiece chars_;
 };
 
+class BoolCharacter {
+  public:
+    BoolCharacter() {}
+
+    explicit BoolCharacter(const bool *delimiter) { delimiter_ = delimiter; }
+
+    StringPiece Find(const StringPiece &in) const {
+      for (const char *i = in.data(); i != in.data() + in.size(); ++i) {
+        if (delimiter_[static_cast<unsigned char>(*i)]) return StringPiece(i, 1);
+      }
+      return StringPiece(in.data() + in.size(), 0);
+    }
+
+  private:
+    const bool *delimiter_;
+};
+
 class AnyCharacterLast {
   public:
     AnyCharacterLast() {}
diff --git a/klm/util/usage.cc b/klm/util/usage.cc
index 8db375e1..e68d7c7c 100644
--- a/klm/util/usage.cc
+++ b/klm/util/usage.cc
@@ -10,61 +10,117 @@
 
 #include <string.h>
 #include <ctype.h>
-#if !defined(_WIN32) && !defined(_WIN64)
+#include <time.h>
+#if defined(_WIN32) || defined(_WIN64)
+// This code lifted from physmem.c in gnulib.  See the copyright statement
+// below.  
+# define WIN32_LEAN_AND_MEAN
+# include <windows.h>
+/*  MEMORYSTATUSEX is missing from older windows headers, so define
+    a local replacement.  */
+typedef struct
+{
+  DWORD dwLength;
+  DWORD dwMemoryLoad;
+  DWORDLONG ullTotalPhys;
+  DWORDLONG ullAvailPhys;
+  DWORDLONG ullTotalPageFile;
+  DWORDLONG ullAvailPageFile;
+  DWORDLONG ullTotalVirtual;
+  DWORDLONG ullAvailVirtual;
+  DWORDLONG ullAvailExtendedVirtual;
+} lMEMORYSTATUSEX;
+typedef WINBOOL (WINAPI *PFN_MS_EX) (lMEMORYSTATUSEX*);
+#else
 #include <sys/resource.h>
 #include <sys/time.h>
-#include <time.h>
 #include <unistd.h>
 #endif
 
-namespace util {
+#if defined(__MACH__) || defined(__FreeBSD__) || defined(__APPLE__)
+#include <sys/types.h>
+#include <sys/sysctl.h>
+#endif
 
-#if !defined(_WIN32) && !defined(_WIN64)
+namespace util {
 namespace {
 
-// On Mac OS X, clock_gettime is not implemented.
-// CLOCK_MONOTONIC is not defined either.
-#ifdef __MACH__
-#define CLOCK_MONOTONIC 0
-
-int clock_gettime(int clk_id, struct timespec *tp) {
+#if defined(__MACH__)
+typedef struct timeval Wall;
+Wall GetWall() {
   struct timeval tv;
   gettimeofday(&tv, NULL);
-  tp->tv_sec = tv.tv_sec;
-  tp->tv_nsec = tv.tv_usec * 1000;
-  return 0;
+  return tv;
 }
-#endif // __MACH__
-
-float FloatSec(const struct timeval &tv) {
-  return static_cast<float>(tv.tv_sec) + (static_cast<float>(tv.tv_usec) / 1000000.0);
+#elif defined(_WIN32) || defined(_WIN64)
+typedef time_t Wall;
+Wall GetWall() {
+  return time(NULL);
 }
-float FloatSec(const struct timespec &tv) {
-  return static_cast<float>(tv.tv_sec) + (static_cast<float>(tv.tv_nsec) / 1000000000.0);
+#else
+typedef struct timespec Wall;
+Wall GetWall() {
+  Wall ret;
+  clock_gettime(CLOCK_MONOTONIC, &ret);
+  return ret;
 }
+#endif
 
-const char *SkipSpaces(const char *at) {
-  for (; *at == ' ' || *at == '\t'; ++at) {}
-  return at;
+// Some of these functions are only used on some platforms.
+#ifdef __clang__
+#pragma clang diagnostic push
+#pragma clang diagnostic ignored "-Wunused-function"
+#endif
+// These all assume first > second
+double Subtract(time_t first, time_t second) {
+  return difftime(first, second);
+}
+double DoubleSec(time_t tv) {
+  return static_cast<double>(tv);
+}
+#if !defined(_WIN32) && !defined(_WIN64)
+double Subtract(const struct timeval &first, const struct timeval &second) {
+  return static_cast<double>(first.tv_sec - second.tv_sec) + static_cast<double>(first.tv_usec - second.tv_usec) / 1000000.0;
 }
+double Subtract(const struct timespec &first, const struct timespec &second) {
+  return static_cast<double>(first.tv_sec - second.tv_sec) + static_cast<double>(first.tv_nsec - second.tv_nsec) / 1000000000.0;
+}
+double DoubleSec(const struct timeval &tv) {
+  return static_cast<double>(tv.tv_sec) + (static_cast<double>(tv.tv_usec) / 1000000.0);
+}
+double DoubleSec(const struct timespec &tv) {
+  return static_cast<double>(tv.tv_sec) + (static_cast<double>(tv.tv_nsec) / 1000000000.0);
+}
+#endif
+#ifdef __clang__
+#pragma clang diagnostic pop
+#endif
 
 class RecordStart {
   public:
     RecordStart() {
-      clock_gettime(CLOCK_MONOTONIC, &started_);
+      started_ = GetWall();
     }
 
-    const struct timespec &Started() const {
+    const Wall &Started() const {
       return started_;
     }
 
   private:
-    struct timespec started_;
+    Wall started_;
 };
 
 const RecordStart kRecordStart;
+
+const char *SkipSpaces(const char *at) {
+  for (; *at == ' ' || *at == '\t'; ++at) {}
+  return at;
+}
 } // namespace
-#endif
+
+double WallTime() {
+  return Subtract(GetWall(), kRecordStart.Started());
+}
 
 void PrintUsage(std::ostream &out) {
 #if !defined(_WIN32) && !defined(_WIN64)
@@ -83,32 +139,89 @@ void PrintUsage(std::ostream &out) {
   }
 
   struct rusage usage;
-  if (getrusage(RUSAGE_CHILDREN, &usage)) {
+  if (getrusage(RUSAGE_SELF, &usage)) {
     perror("getrusage");
     return;
   }
   out << "RSSMax:" << usage.ru_maxrss << " kB" << '\t';
-  out << "user:" << FloatSec(usage.ru_utime) << "\tsys:" << FloatSec(usage.ru_stime) << '\t';
-  out << "CPU:" << (FloatSec(usage.ru_utime) + FloatSec(usage.ru_stime));
-
-  struct timespec current;
-  clock_gettime(CLOCK_MONOTONIC, &current);
-  out << "\treal:" << (FloatSec(current) - FloatSec(kRecordStart.Started())) << '\n';
+  out << "user:" << DoubleSec(usage.ru_utime) << "\tsys:" << DoubleSec(usage.ru_stime) << '\t';
+  out << "CPU:" << (DoubleSec(usage.ru_utime) + DoubleSec(usage.ru_stime));
+  out << '\t';
 #endif
+
+  out << "real:" << WallTime() << '\n';
 }
 
+/* Adapted from physmem.c in gnulib 831b84c59ef413c57a36b67344467d66a8a2ba70 */
+/* Calculate the size of physical memory.
+
+   Copyright (C) 2000-2001, 2003, 2005-2006, 2009-2013 Free Software
+   Foundation, Inc.
+
+   This program is free software: you can redistribute it and/or modify
+   it under the terms of the GNU Lesser General Public License as published by
+   the Free Software Foundation; either version 2.1 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 Lesser General Public License for more details.
+
+   You should have received a copy of the GNU Lesser General Public License
+   along with this program.  If not, see <http://www.gnu.org/licenses/>.  */
+
+/* Written by Paul Eggert.  */
 uint64_t GuessPhysicalMemory() {
+#if defined(_SC_PHYS_PAGES) && defined(_SC_PAGESIZE)
+  {
+    long pages = sysconf(_SC_PHYS_PAGES);
+    long page_size = sysconf(_SC_PAGESIZE);
+    if (pages != -1 && page_size != -1)
+      return static_cast<uint64_t>(pages) * static_cast<uint64_t>(page_size);
+  }
+#endif
+#ifdef HW_PHYSMEM
+  { /* This works on *bsd and darwin.  */
+    unsigned int physmem;
+    size_t len = sizeof physmem;
+    static int mib[2] = { CTL_HW, HW_PHYSMEM };
+
+    if (sysctl (mib, sizeof(mib) / sizeof(mib[0]), &physmem, &len, NULL, 0) == 0
+        && len == sizeof (physmem))
+      return static_cast<uint64_t>(physmem);
+  }
+#endif
+
 #if defined(_WIN32) || defined(_WIN64)
-  return 0;
-#elif defined(_SC_PHYS_PAGES) && defined(_SC_PAGESIZE)
-  long pages = sysconf(_SC_PHYS_PAGES);
-  if (pages == -1) return 0;
-  long page_size = sysconf(_SC_PAGESIZE);
-  if (page_size == -1) return 0;
-  return static_cast<uint64_t>(pages) * static_cast<uint64_t>(page_size);
-#else
-  return 0;
+  { /* this works on windows */
+    PFN_MS_EX pfnex;
+    HMODULE h = GetModuleHandle ("kernel32.dll");
+
+    if (!h)
+      return 0;
+
+    /*  Use GlobalMemoryStatusEx if available.  */
+    if ((pfnex = (PFN_MS_EX) GetProcAddress (h, "GlobalMemoryStatusEx")))
+      {
+        lMEMORYSTATUSEX lms_ex;
+        lms_ex.dwLength = sizeof lms_ex;
+        if (!pfnex (&lms_ex))
+          return 0;
+        return lms_ex.ullTotalPhys;
+      }
+
+    /*  Fall back to GlobalMemoryStatus which is always available.
+        but returns wrong results for physical memory > 4GB.  */
+    else
+      {
+        MEMORYSTATUS ms;
+        GlobalMemoryStatus (&ms);
+        return ms.dwTotalPhys;
+      }
+  }
 #endif
+  return 0;
 }
 
 namespace {
@@ -135,7 +248,7 @@ template <class Num> uint64_t ParseNum(const std::string &arg) {
   if (after == "%") {
     uint64_t mem = GuessPhysicalMemory();
     UTIL_THROW_IF_ARG(!mem, SizeParseError, (arg), "because % was specified but the physical memory size could not be determined.");
-    return static_cast<double>(value) * static_cast<double>(mem) / 100.0;
+    return static_cast<uint64_t>(static_cast<double>(value) * static_cast<double>(mem) / 100.0);
   }
   
   std::string units("bKMGTPEZY");
@@ -144,7 +257,7 @@ template <class Num> uint64_t ParseNum(const std::string &arg) {
   for (std::string::size_type i = 0; i < index; ++i) {
     value *= 1024;
   }
-  return value;
+  return static_cast<uint64_t>(value);
 }
 
 } // namespace
diff --git a/klm/util/usage.hh b/klm/util/usage.hh
index e19eda7b..da53b9e3 100644
--- a/klm/util/usage.hh
+++ b/klm/util/usage.hh
@@ -7,6 +7,9 @@
 #include <stdint.h>
 
 namespace util {
+// Time in seconds since process started.  Zero on unsupported platforms.
+double WallTime();
+
 void PrintUsage(std::ostream &to);
 
 // Determine how much physical memory there is.  Return 0 on failure.