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<a href="GzipIfstream_8h.html">Go to the documentation of this file.</a><div class="fragment"><div class="line"><a name="l00001"></a><span class="lineno"> 1</span> <span class="comment">// --------------------------------------------------------------------------</span></div>
<div class="line"><a name="l00002"></a><span class="lineno"> 2</span> <span class="comment">// OpenMS -- Open-Source Mass Spectrometry</span></div>
<div class="line"><a name="l00003"></a><span class="lineno"> 3</span> <span class="comment">// --------------------------------------------------------------------------</span></div>
<div class="line"><a name="l00004"></a><span class="lineno"> 4</span> <span class="comment">// Copyright The OpenMS Team -- Eberhard Karls University Tuebingen,</span></div>
<div class="line"><a name="l00005"></a><span class="lineno"> 5</span> <span class="comment">// ETH Zurich, and Freie Universitaet Berlin 2002-2013.</span></div>
<div class="line"><a name="l00006"></a><span class="lineno"> 6</span> <span class="comment">//</span></div>
<div class="line"><a name="l00007"></a><span class="lineno"> 7</span> <span class="comment">// This software is released under a three-clause BSD license:</span></div>
<div class="line"><a name="l00008"></a><span class="lineno"> 8</span> <span class="comment">// * Redistributions of source code must retain the above copyright</span></div>
<div class="line"><a name="l00009"></a><span class="lineno"> 9</span> <span class="comment">// notice, this list of conditions and the following disclaimer.</span></div>
<div class="line"><a name="l00010"></a><span class="lineno"> 10</span> <span class="comment">// * Redistributions in binary form must reproduce the above copyright</span></div>
<div class="line"><a name="l00011"></a><span class="lineno"> 11</span> <span class="comment">// notice, this list of conditions and the following disclaimer in the</span></div>
<div class="line"><a name="l00012"></a><span class="lineno"> 12</span> <span class="comment">// documentation and/or other materials provided with the distribution.</span></div>
<div class="line"><a name="l00013"></a><span class="lineno"> 13</span> <span class="comment">// * Neither the name of any author or any participating institution</span></div>
<div class="line"><a name="l00014"></a><span class="lineno"> 14</span> <span class="comment">// may be used to endorse or promote products derived from this software</span></div>
<div class="line"><a name="l00015"></a><span class="lineno"> 15</span> <span class="comment">// without specific prior written permission.</span></div>
<div class="line"><a name="l00016"></a><span class="lineno"> 16</span> <span class="comment">// For a full list of authors, refer to the file AUTHORS.</span></div>
<div class="line"><a name="l00017"></a><span class="lineno"> 17</span> <span class="comment">// --------------------------------------------------------------------------</span></div>
<div class="line"><a name="l00018"></a><span class="lineno"> 18</span> <span class="comment">// THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS"</span></div>
<div class="line"><a name="l00019"></a><span class="lineno"> 19</span> <span class="comment">// AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE</span></div>
<div class="line"><a name="l00020"></a><span class="lineno"> 20</span> <span class="comment">// IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE</span></div>
<div class="line"><a name="l00021"></a><span class="lineno"> 21</span> <span class="comment">// ARE DISCLAIMED. IN NO EVENT SHALL ANY OF THE AUTHORS OR THE CONTRIBUTING</span></div>
<div class="line"><a name="l00022"></a><span class="lineno"> 22</span> <span class="comment">// INSTITUTIONS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL,</span></div>
<div class="line"><a name="l00023"></a><span class="lineno"> 23</span> <span class="comment">// EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO,</span></div>
<div class="line"><a name="l00024"></a><span class="lineno"> 24</span> <span class="comment">// PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS;</span></div>
<div class="line"><a name="l00025"></a><span class="lineno"> 25</span> <span class="comment">// OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY,</span></div>
<div class="line"><a name="l00026"></a><span class="lineno"> 26</span> <span class="comment">// WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR</span></div>
<div class="line"><a name="l00027"></a><span class="lineno"> 27</span> <span class="comment">// OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF</span></div>
<div class="line"><a name="l00028"></a><span class="lineno"> 28</span> <span class="comment">// ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.</span></div>
<div class="line"><a name="l00029"></a><span class="lineno"> 29</span> <span class="comment">//</span></div>
<div class="line"><a name="l00030"></a><span class="lineno"> 30</span> <span class="comment">// --------------------------------------------------------------------------</span></div>
<div class="line"><a name="l00031"></a><span class="lineno"> 31</span> <span class="comment">// $Maintainer: David Wojnar $</span></div>
<div class="line"><a name="l00032"></a><span class="lineno"> 32</span> <span class="comment">// $Authors: David Wojnar $</span></div>
<div class="line"><a name="l00033"></a><span class="lineno"> 33</span> <span class="comment">// --------------------------------------------------------------------------</span></div>
<div class="line"><a name="l00034"></a><span class="lineno"> 34</span> </div>
<div class="line"><a name="l00035"></a><span class="lineno"> 35</span> <span class="preprocessor">#ifndef OPENMS_FORMAT_GZIPIFSTREAM_H</span></div>
<div class="line"><a name="l00036"></a><span class="lineno"> 36</span> <span class="preprocessor"></span><span class="preprocessor">#define OPENMS_FORMAT_GZIPIFSTREAM_H</span></div>
<div class="line"><a name="l00037"></a><span class="lineno"> 37</span> <span class="preprocessor"></span></div>
<div class="line"><a name="l00038"></a><span class="lineno"> 38</span> <span class="preprocessor">#include <OpenMS/config.h></span></div>
<div class="line"><a name="l00039"></a><span class="lineno"> 39</span> <span class="preprocessor">#include <zlib.h></span></div>
<div class="line"><a name="l00040"></a><span class="lineno"> 40</span> </div>
<div class="line"><a name="l00041"></a><span class="lineno"> 41</span> <span class="keyword">namespace </span>OpenMS</div>
<div class="line"><a name="l00042"></a><span class="lineno"> 42</span> {</div>
<div class="line"><a name="l00046"></a><span class="lineno"><a class="line" href="classOpenMS_1_1GzipIfstream.html"> 46</a></span>  <span class="keyword">class </span>OPENMS_DLLAPI <a class="code" href="classOpenMS_1_1GzipIfstream.html">GzipIfstream</a></div>
<div class="line"><a name="l00047"></a><span class="lineno"> 47</span>  {</div>
<div class="line"><a name="l00048"></a><span class="lineno"> 48</span> <span class="keyword">public</span>:</div>
<div class="line"><a name="l00050"></a><span class="lineno"> 50</span>  <a class="code" href="classOpenMS_1_1GzipIfstream.html">GzipIfstream</a>();</div>
<div class="line"><a name="l00052"></a><span class="lineno"> 52</span>  <a class="code" href="classOpenMS_1_1GzipIfstream.html">GzipIfstream</a>(<span class="keyword">const</span> <span class="keywordtype">char</span> * filename);</div>
<div class="line"><a name="l00054"></a><span class="lineno"> 54</span>  <span class="keyword">virtual</span> ~<a class="code" href="classOpenMS_1_1GzipIfstream.html">GzipIfstream</a>();</div>
<div class="line"><a name="l00055"></a><span class="lineno"> 55</span> </div>
<div class="line"><a name="l00066"></a><span class="lineno"> 66</span>  <span class="keywordtype">size_t</span> read(<span class="keywordtype">char</span> * s, <span class="keywordtype">size_t</span> n);</div>
<div class="line"><a name="l00067"></a><span class="lineno"> 67</span> </div>
<div class="line"><a name="l00073"></a><span class="lineno"> 73</span>  <span class="keywordtype">bool</span> streamEnd() <span class="keyword">const</span>;</div>
<div class="line"><a name="l00074"></a><span class="lineno"> 74</span> </div>
<div class="line"><a name="l00078"></a><span class="lineno"> 78</span>  <span class="keywordtype">bool</span> isOpen() <span class="keyword">const</span>;</div>
<div class="line"><a name="l00079"></a><span class="lineno"> 79</span> </div>
<div class="line"><a name="l00084"></a><span class="lineno"> 84</span>  <span class="keywordtype">void</span> open(<span class="keyword">const</span> <span class="keywordtype">char</span> * filename);</div>
<div class="line"><a name="l00085"></a><span class="lineno"> 85</span> </div>
<div class="line"><a name="l00089"></a><span class="lineno"> 89</span>  <span class="keywordtype">void</span> close();</div>
<div class="line"><a name="l00090"></a><span class="lineno"> 90</span> </div>
<div class="line"><a name="l00091"></a><span class="lineno"> 91</span>  <span class="comment">/*</span></div>
<div class="line"><a name="l00092"></a><span class="lineno"> 92</span> <span class="comment"> @brief updates crc32 check sum whether the buffer is corrupted</span></div>
<div class="line"><a name="l00093"></a><span class="lineno"> 93</span> <span class="comment"> @note if this function is used it has to be called after every call of function read</span></div>
<div class="line"><a name="l00094"></a><span class="lineno"> 94</span> <span class="comment"> @param s the buffer which will be checked</span></div>
<div class="line"><a name="l00095"></a><span class="lineno"> 95</span> <span class="comment"> @param n the size of the buffer</span></div>
<div class="line"><a name="l00096"></a><span class="lineno"> 96</span> <span class="comment"> *</span></div>
<div class="line"><a name="l00097"></a><span class="lineno"> 97</span> <span class="comment"> //void updateCRC32(const char* s,const size_t n);</span></div>
<div class="line"><a name="l00098"></a><span class="lineno"> 98</span> <span class="comment"></span></div>
<div class="line"><a name="l00099"></a><span class="lineno"> 99</span> <span class="comment"> *</span></div>
<div class="line"><a name="l00100"></a><span class="lineno"> 100</span> <span class="comment"> @brief checks if data is corrupted after crc32 was computed</span></div>
<div class="line"><a name="l00101"></a><span class="lineno"> 101</span> <span class="comment"> @note it can only be used if updateCRC32 was called after every call of function read</span></div>
<div class="line"><a name="l00102"></a><span class="lineno"> 102</span> <span class="comment"> @return true if the buffer and hence the file is corrupted; no decompression is possible</span></div>
<div class="line"><a name="l00103"></a><span class="lineno"> 103</span> <span class="comment"> *</span></div>
<div class="line"><a name="l00104"></a><span class="lineno"> 104</span> <span class="comment"> //bool isCorrupted();</span></div>
<div class="line"><a name="l00105"></a><span class="lineno"> 105</span> <span class="comment"></span></div>
<div class="line"><a name="l00106"></a><span class="lineno"> 106</span> <span class="comment"> //unsigned long Crc32_ComputeBuf( unsigned long inCrc32, const void *buf,</span></div>
<div class="line"><a name="l00107"></a><span class="lineno"> 107</span> <span class="comment">// size_t bufLen );*/</span></div>
<div class="line"><a name="l00108"></a><span class="lineno"> 108</span> </div>
<div class="line"><a name="l00109"></a><span class="lineno"> 109</span> <span class="keyword">protected</span>:</div>
<div class="line"><a name="l00110"></a><span class="lineno"> 110</span> </div>
<div class="line"><a name="l00112"></a><span class="lineno"><a class="line" href="classOpenMS_1_1GzipIfstream.html#a1ef1df9742bd5e857368e642d08abe8b"> 112</a></span>  gzFile <a class="code" href="classOpenMS_1_1GzipIfstream.html#a1ef1df9742bd5e857368e642d08abe8b">gzfile_</a>;</div>
<div class="line"><a name="l00114"></a><span class="lineno"><a class="line" href="classOpenMS_1_1GzipIfstream.html#a0a69ff8a0cfdfed54d396db4b1d52500"> 114</a></span>  <span class="keywordtype">int</span> <a class="code" href="classOpenMS_1_1GzipIfstream.html#a0a69ff8a0cfdfed54d396db4b1d52500">n_buffer_</a>;</div>
<div class="line"><a name="l00116"></a><span class="lineno"><a class="line" href="classOpenMS_1_1GzipIfstream.html#a0180727fb53abbbb970c35e80965e3fb"> 116</a></span>  <span class="keywordtype">int</span> <a class="code" href="classOpenMS_1_1GzipIfstream.html#a0180727fb53abbbb970c35e80965e3fb">gzerror_</a>;</div>
<div class="line"><a name="l00118"></a><span class="lineno"><a class="line" href="classOpenMS_1_1GzipIfstream.html#a5bc5b565c935f4accdf0d7d240301bdc"> 118</a></span>  <span class="keywordtype">bool</span> <a class="code" href="classOpenMS_1_1GzipIfstream.html#a5bc5b565c935f4accdf0d7d240301bdc">stream_at_end_</a>;</div>
<div class="line"><a name="l00119"></a><span class="lineno"> 119</span> </div>
<div class="line"><a name="l00120"></a><span class="lineno"> 120</span>  <span class="comment">//needed if one wants to know whetther file is okay</span></div>
<div class="line"><a name="l00121"></a><span class="lineno"> 121</span>  <span class="comment">//unsigned long original_crc;</span></div>
<div class="line"><a name="l00122"></a><span class="lineno"> 122</span>  <span class="comment">//needed if one wants to know whetther file is okay</span></div>
<div class="line"><a name="l00123"></a><span class="lineno"> 123</span>  <span class="comment">//unsigned long crc;</span></div>
<div class="line"><a name="l00124"></a><span class="lineno"> 124</span> </div>
<div class="line"><a name="l00126"></a><span class="lineno"> 126</span>  <a class="code" href="classOpenMS_1_1GzipIfstream.html">GzipIfstream</a>(<span class="keyword">const</span> <a class="code" href="classOpenMS_1_1GzipIfstream.html">GzipIfstream</a> & bzip2);</div>
<div class="line"><a name="l00127"></a><span class="lineno"> 127</span>  <a class="code" href="classOpenMS_1_1GzipIfstream.html">GzipIfstream</a> & operator=(<span class="keyword">const</span> <a class="code" href="classOpenMS_1_1GzipIfstream.html">GzipIfstream</a> & bzip2);</div>
<div class="line"><a name="l00128"></a><span class="lineno"> 128</span>  };</div>
<div class="line"><a name="l00129"></a><span class="lineno"> 129</span> </div>
<div class="line"><a name="l00130"></a><span class="lineno"><a class="line" href="classOpenMS_1_1GzipIfstream.html#a3c7351cec1380d07f9e4b3ec96b2b1ff"> 130</a></span>  <span class="keyword">inline</span> <span class="keywordtype">bool</span> <a class="code" href="classOpenMS_1_1GzipIfstream.html#a3c7351cec1380d07f9e4b3ec96b2b1ff">GzipIfstream::isOpen</a>()<span class="keyword"> const</span></div>
<div class="line"><a name="l00131"></a><span class="lineno"> 131</span> <span class="keyword"> </span>{</div>
<div class="line"><a name="l00132"></a><span class="lineno"> 132</span>  <span class="keywordflow">return</span> <a class="code" href="classOpenMS_1_1GzipIfstream.html#a1ef1df9742bd5e857368e642d08abe8b">gzfile_</a> != <a class="code" href="IsotopeWaveletParallelFor_8h.html#a070d2ce7b6bb7e5c05602aa8c308d0c4">NULL</a>;</div>
<div class="line"><a name="l00133"></a><span class="lineno"> 133</span>  }</div>
<div class="line"><a name="l00134"></a><span class="lineno"> 134</span> </div>
<div class="line"><a name="l00135"></a><span class="lineno"><a class="line" href="classOpenMS_1_1GzipIfstream.html#a5e93134387edbe53b3ae66852a37eb1f"> 135</a></span>  <span class="keyword">inline</span> <span class="keywordtype">bool</span> <a class="code" href="classOpenMS_1_1GzipIfstream.html#a5e93134387edbe53b3ae66852a37eb1f">GzipIfstream::streamEnd</a>()<span class="keyword"> const</span></div>
<div class="line"><a name="l00136"></a><span class="lineno"> 136</span> <span class="keyword"> </span>{</div>
<div class="line"><a name="l00137"></a><span class="lineno"> 137</span>  <span class="keywordflow">return</span> <a class="code" href="classOpenMS_1_1GzipIfstream.html#a5bc5b565c935f4accdf0d7d240301bdc">stream_at_end_</a>;</div>
<div class="line"><a name="l00138"></a><span class="lineno"> 138</span>  }</div>
<div class="line"><a name="l00139"></a><span class="lineno"> 139</span> </div>
<div class="line"><a name="l00140"></a><span class="lineno"> 140</span> <span class="comment">/* inline bool GzipIfstream::isCorrupted()</span></div>
<div class="line"><a name="l00141"></a><span class="lineno"> 141</span> <span class="comment"> {</span></div>
<div class="line"><a name="l00142"></a><span class="lineno"> 142</span> <span class="comment"> std::cout<<"CRC"<<crc<<std::endl;</span></div>
<div class="line"><a name="l00143"></a><span class="lineno"> 143</span> <span class="comment"> return (crc != original_crc);</span></div>
<div class="line"><a name="l00144"></a><span class="lineno"> 144</span> <span class="comment"> }*/</span></div>
<div class="line"><a name="l00145"></a><span class="lineno"> 145</span> </div>
<div class="line"><a name="l00146"></a><span class="lineno"> 146</span> } <span class="comment">//namespace OpenMS</span></div>
<div class="line"><a name="l00147"></a><span class="lineno"> 147</span> <span class="preprocessor">#endif //OPENMS_FORMAT_GZIPIFSTREAM_H</span></div>
<div class="ttc" id="classOpenMS_1_1GzipIfstream_html"><div class="ttname"><a href="classOpenMS_1_1GzipIfstream.html">OpenMS::GzipIfstream</a></div><div class="ttdoc">Decompresses files which are compressed in the gzip format (*.gzip) </div><div class="ttdef"><b>Definition:</b> GzipIfstream.h:46</div></div>
<div class="ttc" id="classOpenMS_1_1GzipIfstream_html_a5bc5b565c935f4accdf0d7d240301bdc"><div class="ttname"><a href="classOpenMS_1_1GzipIfstream.html#a5bc5b565c935f4accdf0d7d240301bdc">OpenMS::GzipIfstream::stream_at_end_</a></div><div class="ttdeci">bool stream_at_end_</div><div class="ttdoc">true if end of file is reached </div><div class="ttdef"><b>Definition:</b> GzipIfstream.h:118</div></div>
<div class="ttc" id="IsotopeWaveletParallelFor_8h_html_a070d2ce7b6bb7e5c05602aa8c308d0c4"><div class="ttname"><a href="IsotopeWaveletParallelFor_8h.html#a070d2ce7b6bb7e5c05602aa8c308d0c4">NULL</a></div><div class="ttdeci">#define NULL</div><div class="ttdef"><b>Definition:</b> IsotopeWaveletParallelFor.h:41</div></div>
<div class="ttc" id="classOpenMS_1_1GzipIfstream_html_a0180727fb53abbbb970c35e80965e3fb"><div class="ttname"><a href="classOpenMS_1_1GzipIfstream.html#a0180727fb53abbbb970c35e80965e3fb">OpenMS::GzipIfstream::gzerror_</a></div><div class="ttdeci">int gzerror_</div><div class="ttdoc">saves the last returned error by the read function </div><div class="ttdef"><b>Definition:</b> GzipIfstream.h:116</div></div>
<div class="ttc" id="classOpenMS_1_1GzipIfstream_html_a5e93134387edbe53b3ae66852a37eb1f"><div class="ttname"><a href="classOpenMS_1_1GzipIfstream.html#a5e93134387edbe53b3ae66852a37eb1f">OpenMS::GzipIfstream::streamEnd</a></div><div class="ttdeci">bool streamEnd() const </div><div class="ttdoc">indicates whether the read function can be used safely </div><div class="ttdef"><b>Definition:</b> GzipIfstream.h:135</div></div>
<div class="ttc" id="classOpenMS_1_1GzipIfstream_html_a1ef1df9742bd5e857368e642d08abe8b"><div class="ttname"><a href="classOpenMS_1_1GzipIfstream.html#a1ef1df9742bd5e857368e642d08abe8b">OpenMS::GzipIfstream::gzfile_</a></div><div class="ttdeci">gzFile gzfile_</div><div class="ttdoc">a gzFile object(void*) . Necessary for decompression </div><div class="ttdef"><b>Definition:</b> GzipIfstream.h:112</div></div>
<div class="ttc" id="classOpenMS_1_1GzipIfstream_html_a0a69ff8a0cfdfed54d396db4b1d52500"><div class="ttname"><a href="classOpenMS_1_1GzipIfstream.html#a0a69ff8a0cfdfed54d396db4b1d52500">OpenMS::GzipIfstream::n_buffer_</a></div><div class="ttdeci">int n_buffer_</div><div class="ttdoc">counts the last read bufffer </div><div class="ttdef"><b>Definition:</b> GzipIfstream.h:114</div></div>
<div class="ttc" id="classOpenMS_1_1GzipIfstream_html_a3c7351cec1380d07f9e4b3ec96b2b1ff"><div class="ttname"><a href="classOpenMS_1_1GzipIfstream.html#a3c7351cec1380d07f9e4b3ec96b2b1ff">OpenMS::GzipIfstream::isOpen</a></div><div class="ttdeci">bool isOpen() const </div><div class="ttdoc">returns whether a file is open. </div><div class="ttdef"><b>Definition:</b> GzipIfstream.h:130</div></div>
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<TD><font color="#c0c0c0">OpenMS / TOPP release 1.11.1</font></TD>
<TD align="right"><font color="#c0c0c0">Documentation generated on Thu Nov 14 2013 11:19:14 using doxygen 1.8.5</font></TD>
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