Replace fdstream implementation with a stock one wnd work out that GC…

…SAs can't be serialized empty

LICENSE

@@ -22,7 +22,7 @@ COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER LIABILITY, WHETHER
 IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM, OUT OF OR IN
 CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE SOFTWARE.
 
-Catch.hpp is licensed under the Boost Software License.
+src/unittest/catch.hpp is licensed under the Boost Software License.
 
 Boost Software License - Version 1.0 - August 17th, 2003
 
@@ -47,3 +47,11 @@ SHALL THE COPYRIGHT HOLDERS OR ANYONE DISTRIBUTING THE SOFTWARE BE LIABLE
 FOR ANY DAMAGES OR OTHER LIABILITY, WHETHER IN CONTRACT, TORT OR OTHERWISE,
 ARISING FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER
 DEALINGS IN THE SOFTWARE.
+
+src/stream/fdstream.hpp is licensed under the following license:
+
+(C) Copyright Nicolai M. Josuttis 2001.
+Permission to copy, use, modify, sell and distribute this software
+is granted provided this copyright notice appears in all copies.
+This software is provided "as is" without express or implied
+warranty, and with no claim as to its suitability for any purpose.

src/stream/fdstream.hpp

@@ -0,0 +1,188 @@
+/* The following code declares classes to read from and write to
+ * file descriptore or file handles.
+ *
+ * See
+ *      http://www.josuttis.com/cppcode
+ * for details and the latest version.
+ *
+ * - open:
+ *      - integrating BUFSIZ on some systems?
+ *      - optimized reading of multiple characters
+ *      - stream for reading AND writing
+ *      - i18n
+ *
+ * (C) Copyright Nicolai M. Josuttis 2001.
+ * Permission to copy, use, modify, sell and distribute this software
+ * is granted provided this copyright notice appears in all copies.
+ * This software is provided "as is" without express or implied
+ * warranty, and with no claim as to its suitability for any purpose.
+ *
+ * Version: Jul 28, 2002
+ * History:
+ *  Jan 29, 2019: namespace for vg project
+ *  Jul 28, 2002: bugfix memcpy() => memmove()
+ *                fdinbuf::underflow(): cast for return statements
+ *  Aug 05, 2001: first public version
+ */
+#ifndef VG_STREAM_FDSTREAM_HPP_INCLUDED
+#define VG_STREAM_FDSTREAM_HPP_INCLUDED
+
+#include <istream>
+#include <ostream>
+#include <streambuf>
+// for EOF:
+#include <cstdio>
+// for memmove():
+#include <cstring>
+
+
+// low-level read and write functions
+#ifdef _MSC_VER
+# include <io.h>
+#else
+# include <unistd.h>
+//extern "C" {
+//    int write (int fd, const char* buf, int num);
+//    int read (int fd, char* buf, int num);
+//}
+#endif
+
+
+namespace vg {
+
+namespace stream {
+
+
+/************************************************************
+ * fdostream
+ * - a stream that writes on a file descriptor
+ ************************************************************/
+
+
+class fdoutbuf : public std::streambuf {
+  protected:
+    int fd;    // file descriptor
+  public:
+    // constructor
+    fdoutbuf (int _fd) : fd(_fd) {
+    }
+  protected:
+    // write one character
+    virtual int_type overflow (int_type c) {
+        if (c != EOF) {
+            char z = c;
+            if (write (fd, &z, 1) != 1) {
+                return EOF;
+            }
+        }
+        return c;
+    }
+    // write multiple characters
+    virtual
+    std::streamsize xsputn (const char* s,
+                            std::streamsize num) {
+        return write(fd,s,num);
+    }
+};
+
+class fdostream : public std::ostream {
+  protected:
+    fdoutbuf buf;
+  public:
+    fdostream (int fd) : std::ostream(0), buf(fd) {
+        rdbuf(&buf);
+    }
+};
+
+
+/************************************************************
+ * fdistream
+ * - a stream that reads on a file descriptor
+ ************************************************************/
+
+class fdinbuf : public std::streambuf {
+  protected:
+    int fd;    // file descriptor
+  protected:
+    /* data buffer:
+     * - at most, pbSize characters in putback area plus
+     * - at most, bufSize characters in ordinary read buffer
+     */
+    static const int pbSize = 4;        // size of putback area
+    static const int bufSize = 1024;    // size of the data buffer
+    char buffer[bufSize+pbSize];        // data buffer
+
+  public:
+    /* constructor
+     * - initialize file descriptor
+     * - initialize empty data buffer
+     * - no putback area
+     * => force underflow()
+     */
+    fdinbuf (int _fd) : fd(_fd) {
+        setg (buffer+pbSize,     // beginning of putback area
+              buffer+pbSize,     // read position
+              buffer+pbSize);    // end position
+    }
+
+  protected:
+    // insert new characters into the buffer
+    virtual int_type underflow () {
+#ifndef _MSC_VER
+        using std::memmove;
+#endif
+
+        // is read position before end of buffer?
+        if (gptr() < egptr()) {
+            return traits_type::to_int_type(*gptr());
+        }
+
+        /* process size of putback area
+         * - use number of characters read
+         * - but at most size of putback area
+         */
+        int numPutback;
+        numPutback = gptr() - eback();
+        if (numPutback > pbSize) {
+            numPutback = pbSize;
+        }
+
+        /* copy up to pbSize characters previously read into
+         * the putback area
+         */
+        memmove (buffer+(pbSize-numPutback), gptr()-numPutback,
+                numPutback);
+
+        // read at most bufSize new characters
+        int num;
+        num = read (fd, buffer+pbSize, bufSize);
+        if (num <= 0) {
+            // ERROR or EOF
+            return EOF;
+        }
+
+        // reset buffer pointers
+        setg (buffer+(pbSize-numPutback),   // beginning of putback area
+              buffer+pbSize,                // read position
+              buffer+pbSize+num);           // end of buffer
+
+        // return next character
+        return traits_type::to_int_type(*gptr());
+    }
+};
+
+class fdistream : public std::istream {
+  protected:
+    fdinbuf buf;
+  public:
+    fdistream (int fd) : std::istream(0), buf(fd) {
+        rdbuf(&buf);
+    }
+};
+
+
+}
+
+}
+
+#endif

src/stream/register_loader_saver_gcsa.cpp

@@ -26,7 +26,8 @@ void register_loader_saver_gcsa() {
         return (void*) index;
     }), wrap_stream_saver([](const void* index_void, ostream& output) {
         // Cast to GCSA and serialize to the stream.
-        sdsl::serialize(*(const gcsa::GCSA*) index_void, output);
+        assert(index_void != nullptr);
+        ((const gcsa::GCSA*) index_void)->serialize(output);
     }));
 }
 

src/stream/register_loader_saver_lcp.cpp

@@ -26,7 +26,7 @@ void register_loader_saver_lcp() {
         return (void*) index;
     }), wrap_stream_saver([](const void* index_void, ostream& output) {
         // Cast to LCP and serialize to the stream.
-        sdsl::serialize(*(const gcsa::LCPArray*) index_void, output);
+        ((const gcsa::LCPArray*) index_void)->serialize(output);
     }));
 
 }