RDKit
Open-source cheminformatics and machine learning.
StreamOps.h
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1 //
2 // Copyright (C) 2002-2008 Greg Landrum and Rational Discovery LLC
3 //
4 // @@ All Rights Reserved @@
5 // This file is part of the RDKit.
6 // The contents are covered by the terms of the BSD license
7 // which is included in the file license.txt, found at the root
8 // of the RDKit source tree.
9 //
10 //
11 #ifndef _RD_STREAMOPS_H
12 #define _RD_STREAMOPS_H
13 
14 #include "types.h"
15 #include <string>
16 #include <sstream>
17 #include <iostream>
18 #include <boost/cstdint.hpp>
19 #include <boost/detail/endian.hpp>
20 
21 namespace RDKit {
22 // this code block for handling endian problems is from :
23 // http://stackoverflow.com/questions/105252/how-do-i-convert-between-big-endian-and-little-endian-values-in-c
24 enum EEndian {
27 #if defined(BOOST_LITTLE_ENDIAN)
28  HOST_ENDIAN_ORDER = LITTLE_ENDIAN_ORDER
29 #elif defined(BOOST_BIG_ENDIAN)
30  HOST_ENDIAN_ORDER = BIG_ENDIAN_ORDER
31 #else
32 #error "Failed to determine the system endian value"
33 #endif
34 };
35 
36 // this function swap the bytes of values given it's size as a template
37 // parameter (could sizeof be used?).
38 template <class T, unsigned int size>
39 inline T SwapBytes(T value) {
40  union {
41  T value;
42  char bytes[size];
43  } in, out;
44 
45  in.value = value;
46 
47  for (unsigned int i = 0; i < size / 2; ++i) {
48  out.bytes[i] = in.bytes[size - 1 - i];
49  out.bytes[size - 1 - i] = in.bytes[i];
50  }
51 
52  return out.value;
53 }
54 
55 // Here is the function you will use. Again there is two compile-time assertion
56 // that use the boost librarie. You could probably comment them out, but if you
57 // do be cautious not to use this function for anything else than integers
58 // types. This function need to be calles like this :
59 //
60 // int x = someValue;
61 // int i = EndianSwapBytes<HOST_ENDIAN_ORDER, BIG_ENDIAN_ORDER>(x);
62 //
63 template <EEndian from, EEndian to, class T>
64 inline T EndianSwapBytes(T value) {
65  // A : La donnée à swapper à une taille de 2, 4 ou 8 octets
66  BOOST_STATIC_ASSERT(sizeof(T) == 1 || sizeof(T) == 2 || sizeof(T) == 4 ||
67  sizeof(T) == 8);
68  if (sizeof(T) == 1) return value;
69 
70  // A : La donnée à swapper est d'un type arithmetic
71  // BOOST_STATIC_ASSERT(boost::is_arithmetic<T>::value);
72 
73  // Si from et to sont du même type on ne swap pas.
74  if (from == to) return value;
75 
76  return SwapBytes<T, sizeof(T)>(value);
77 }
78 template <EEndian from, EEndian to>
79 inline char EndianSwapBytes(char value) {
80  return value;
81 }
82 template <EEndian from, EEndian to>
83 inline unsigned char EndianSwapBytes(unsigned char value) {
84  return value;
85 }
86 template <EEndian from, EEndian to>
87 inline signed char EndianSwapBytes(signed char value) {
88  return value;
89 }
90 // --------------------------------------
91 
92 //! Packs an integer and outputs it to a stream
93 inline void appendPackedIntToStream(std::stringstream &ss,
94  boost::uint32_t num) {
95  int nbytes, bix;
96  unsigned int val, res;
97  char tc;
98 
99  res = num;
100  while (1) {
101  if (res < (1 << 7)) {
102  val = (res << 1);
103  nbytes = 1;
104  break;
105  }
106  res -= (1 << 7);
107  if (res < (1 << 14)) {
108  val = ((res << 2) | 1);
109  nbytes = 2;
110  break;
111  }
112  res -= (1 << 14);
113  if (res < (1 << 21)) {
114  val = ((res << 3) | 3);
115  nbytes = 3;
116  break;
117  }
118  res -= (1 << 21);
119  if (res < (1 << 29)) {
120  val = ((res << 3) | 7);
121  nbytes = 4;
122  break;
123  } else {
124  CHECK_INVARIANT(0, "ERROR: Integer too big to pack\n");
125  }
126  }
127  // val = EndianSwapBytes<HOST_ENDIAN_ORDER,LITTLE_ENDIAN_ORDER>(val);
128 
129  for (bix = 0; bix < nbytes; bix++) {
130  tc = (char)(val & 255);
131  ss.write(&tc, 1);
132  val >>= 8;
133  }
134 }
135 
136 //! Reads an integer from a stream in packed format and returns the result.
137 inline boost::uint32_t readPackedIntFromStream(std::stringstream &ss) {
138  boost::uint32_t val, num;
139  int shift, offset;
140  char tmp;
141  ss.read(&tmp, sizeof(tmp));
142  val = UCHAR(tmp);
143  offset = 0;
144  if ((val & 1) == 0) {
145  shift = 1;
146  } else if ((val & 3) == 1) {
147  ss.read((char *)&tmp, sizeof(tmp));
148  val |= (UCHAR(tmp) << 8);
149  shift = 2;
150  offset = (1 << 7);
151  } else if ((val & 7) == 3) {
152  ss.read((char *)&tmp, sizeof(tmp));
153  val |= (UCHAR(tmp) << 8);
154  ss.read((char *)&tmp, sizeof(tmp));
155  val |= (UCHAR(tmp) << 16);
156  shift = 3;
157  offset = (1 << 7) + (1 << 14);
158  } else {
159  ss.read((char *)&tmp, sizeof(tmp));
160  val |= (UCHAR(tmp) << 8);
161  ss.read((char *)&tmp, sizeof(tmp));
162  val |= (UCHAR(tmp) << 16);
163  ss.read((char *)&tmp, sizeof(tmp));
164  val |= (UCHAR(tmp) << 24);
165  shift = 3;
166  offset = (1 << 7) + (1 << 14) + (1 << 21);
167  }
168  num = (val >> shift) + offset;
169  // num = EndianSwapBytes<LITTLE_ENDIAN_ORDER,HOST_ENDIAN_ORDER>(num);
170  return num;
171 }
172 
173 //! Reads an integer from a char * in packed format and returns the result.
174 //! The argument is advanced
175 inline boost::uint32_t pullPackedIntFromString(const char *&text) {
176  boost::uint32_t val, num;
177  int shift, offset;
178  char tmp;
179  tmp = *text;
180  text++;
181  val = UCHAR(tmp);
182  offset = 0;
183  if ((val & 1) == 0) {
184  shift = 1;
185  } else if ((val & 3) == 1) {
186  tmp = *text;
187  text++;
188  val |= (UCHAR(tmp) << 8);
189  shift = 2;
190  offset = (1 << 7);
191  } else if ((val & 7) == 3) {
192  tmp = *text;
193  text++;
194  val |= (UCHAR(tmp) << 8);
195  tmp = *text;
196  text++;
197  val |= (UCHAR(tmp) << 16);
198  shift = 3;
199  offset = (1 << 7) + (1 << 14);
200  } else {
201  tmp = *text;
202  text++;
203  val |= (UCHAR(tmp) << 8);
204  tmp = *text;
205  text++;
206  val |= (UCHAR(tmp) << 16);
207  tmp = *text;
208  text++;
209  val |= (UCHAR(tmp) << 24);
210  shift = 3;
211  offset = (1 << 7) + (1 << 14) + (1 << 21);
212  }
213  num = (val >> shift) + offset;
214  // num = EndianSwapBytes<LITTLE_ENDIAN_ORDER,HOST_ENDIAN_ORDER>(num);
215  return num;
216 }
217 
218 //! does a binary write of an object to a stream
219 template <typename T>
220 void streamWrite(std::ostream &ss, const T &val) {
221  T tval = EndianSwapBytes<HOST_ENDIAN_ORDER, LITTLE_ENDIAN_ORDER>(val);
222  ss.write((const char *)&tval, sizeof(T));
223 }
224 //! does a binary read of an object from a stream
225 template <typename T>
226 void streamRead(std::istream &ss, T &loc) {
227  T tloc;
228  ss.read((char *)&tloc, sizeof(T));
229  loc = EndianSwapBytes<LITTLE_ENDIAN_ORDER, HOST_ENDIAN_ORDER>(tloc);
230 }
231 
232 //! grabs the next line from an instream and returns it.
233 inline std::string getLine(std::istream *inStream) {
234  std::string res;
235  std::getline(*inStream, res);
236  if ((res.length() > 0) && (res[res.length() - 1] == '\r')) {
237  res.erase(res.length() - 1);
238  }
239  return res;
240 }
241 //! grabs the next line from an instream and returns it.
242 inline std::string getLine(std::istream &inStream) {
243  return getLine(&inStream);
244 }
245 }
246 
247 #endif
T EndianSwapBytes(T value)
Definition: StreamOps.h:64
#define CHECK_INVARIANT(expr, mess)
Definition: Invariant.h:99
unsigned char UCHAR
Definition: types.h:186
EEndian
Definition: StreamOps.h:24
void streamRead(std::istream &ss, T &loc)
does a binary read of an object from a stream
Definition: StreamOps.h:226
boost::uint32_t readPackedIntFromStream(std::stringstream &ss)
Reads an integer from a stream in packed format and returns the result.
Definition: StreamOps.h:137
boost::uint32_t pullPackedIntFromString(const char *&text)
Definition: StreamOps.h:175
T SwapBytes(T value)
Definition: StreamOps.h:39
Includes a bunch of functionality for handling Atom and Bond queries.
Definition: Atom.h:29
void streamWrite(std::ostream &ss, const T &val)
does a binary write of an object to a stream
Definition: StreamOps.h:220
std::string getLine(std::istream *inStream)
grabs the next line from an instream and returns it.
Definition: StreamOps.h:233
void appendPackedIntToStream(std::stringstream &ss, boost::uint32_t num)
Packs an integer and outputs it to a stream.
Definition: StreamOps.h:93