new mafft v 6.857 with extensions

[jabaws.git] / binaries / src / mafft / extensions / mxscarna_src / probconsRNA / FileBuffer.h

diff --git a/binaries/src/mafft/extensions/mxscarna_src/probconsRNA/FileBuffer.h b/binaries/src/mafft/extensions/mxscarna_src/probconsRNA/FileBuffer.h
new file mode 100644 (file)
index 0000000..9c36188
--- /dev/null
+++ b/binaries/src/mafft/extensions/mxscarna_src/probconsRNA/FileBuffer.h
@@ -0,0 +1,104 @@
+/////////////////////////////////////////////////////////////////
+// FileBuffer.h
+//
+// Buffered file reading.
+/////////////////////////////////////////////////////////////////
+
+
+#ifndef FILEBUFFER_H
+#define FILEBUFFER_H
+
+#include <string>
+#include <fstream>
+#include <iostream>
+
+using namespace std;
+
+const int BufferSize = 1000;
+
+/////////////////////////////////////////////////////////////////
+// FileBuffer
+//
+// Class for buffering file reading.
+/////////////////////////////////////////////////////////////////
+namespace MXSCARNA {
+class FileBuffer {
+  ifstream file;
+  char buffer[BufferSize];
+  int currPos;
+  int size;
+  bool isEOF;
+  bool isValid;
+  bool canUnget;
+
+ public:
+
+  // Some common routines
+
+  FileBuffer (const char *filename) : file (filename), currPos (0), size (0), isEOF (false), isValid (!file.fail()), canUnget (false){}
+  ~FileBuffer (){ close(); }
+  bool fail () const { return !isValid; }
+  bool eof () const { return (!isValid || isEOF); }
+  void close(){ file.close(); isValid = false; }
+
+  /////////////////////////////////////////////////////////////////
+  // FileBuffer::Get()
+  //
+  // Retrieve a character from the file buffer.  Returns true if
+  // and only if a character is read.
+  /////////////////////////////////////////////////////////////////
+
+  bool Get (char &ch){
+
+    // check to make sure that there's more stuff in the file
+    if (!isValid || isEOF) return false;
+
+    // if the buffer is empty, it's time to reload it
+    if (currPos == size){
+      file.read (buffer, BufferSize);
+      size = file.gcount();
+      isEOF = (size == 0);
+      currPos = 0;
+      if (isEOF) return false;
+    }
+
+    // store the read character
+    ch = buffer[currPos++];
+    canUnget = true;
+    return true;
+  }
+
+  /////////////////////////////////////////////////////////////////
+  // FileBuffer::UnGet()
+  //
+  // Unretrieve the most recently read character from the file
+  // buffer.  Note that this allows only a one-level undo.
+  /////////////////////////////////////////////////////////////////
+
+  void UnGet (){
+    assert (canUnget);
+    assert (isValid);
+    assert (currPos > 0);
+    currPos--;
+    assert (currPos < size);
+    isEOF = false;
+    canUnget = false;
+  }
+
+  /////////////////////////////////////////////////////////////////
+  // FileBuffer::GetLine()
+  //
+  // Retrieve characters of text until a newline character is
+  // encountered.  Terminates properly on end-of-file condition.
+  /////////////////////////////////////////////////////////////////
+
+  void GetLine (string &s){
+    char ch;
+    s = "";
+    while (Get (ch) && ch != '\n')
+      s += ch;
+  }
+
+};
+}
+#endif