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<a href="_i_bam_i_o_device_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">// IBamIODevice.h (c) 2011 Derek Barnett</span></div><div class="line"><a name="l00003"></a><span class="lineno"> 3</span> <span class="comment">// Marth Lab, Department of Biology, Boston College</span></div><div class="line"><a name="l00004"></a><span class="lineno"> 4</span> <span class="comment">// ---------------------------------------------------------------------------</span></div><div class="line"><a name="l00005"></a><span class="lineno"> 5</span> <span class="comment">// Last modified: 10 November 2011 (DB)</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">// Base class for all BAM I/O devices (e.g. local file, pipe, HTTP, FTP, etc.)</span></div><div class="line"><a name="l00008"></a><span class="lineno"> 8</span> <span class="comment">//</span></div><div class="line"><a name="l00009"></a><span class="lineno"> 9</span> <span class="comment">// Derived classes should provide protocol-specific implementations for</span></div><div class="line"><a name="l00010"></a><span class="lineno"> 10</span> <span class="comment">// reading/writing plain bytes, as well as other I/O-related behaviors.</span></div><div class="line"><a name="l00011"></a><span class="lineno"> 11</span> <span class="comment">//</span></div><div class="line"><a name="l00012"></a><span class="lineno"> 12</span> <span class="comment">// Since IBamIODevices may be defined in client code, the internal</span></div><div class="line"><a name="l00013"></a><span class="lineno"> 13</span> <span class="comment">// BamExceptions are NOT allowed to be thrown from devices, including the</span></div><div class="line"><a name="l00014"></a><span class="lineno"> 14</span> <span class="comment">// built-in ones. This keeps a consistent interface at the BgzfStream for</span></div><div class="line"><a name="l00015"></a><span class="lineno"> 15</span> <span class="comment">// handling any device type. Use the error string for relaying error messages.</span></div><div class="line"><a name="l00016"></a><span class="lineno"> 16</span> <span class="comment">// ***************************************************************************</span></div><div class="line"><a name="l00017"></a><span class="lineno"> 17</span> </div><div class="line"><a name="l00018"></a><span class="lineno"> 18</span> <span class="preprocessor">#ifndef IBAMIODEVICE_H</span></div><div class="line"><a name="l00019"></a><span class="lineno"> 19</span> <span class="preprocessor">#define IBAMIODEVICE_H</span></div><div class="line"><a name="l00020"></a><span class="lineno"> 20</span> </div><div class="line"><a name="l00021"></a><span class="lineno"> 21</span> <span class="preprocessor">#include "<a class="code" href="api__global_8h.html">api/api_global.h</a>"</span></div><div class="line"><a name="l00022"></a><span class="lineno"> 22</span> <span class="preprocessor">#include <cstdio></span></div><div class="line"><a name="l00023"></a><span class="lineno"> 23</span> <span class="preprocessor">#include <string></span></div><div class="line"><a name="l00024"></a><span class="lineno"> 24</span> </div><div class="line"><a name="l00025"></a><span class="lineno"> 25</span> <span class="keyword">namespace </span><a class="code" href="namespace_bam_tools.html">BamTools</a> {</div><div class="line"><a name="l00026"></a><span class="lineno"> 26</span> </div><div class="line"><a name="l00027"></a><span class="lineno"><a class="line" href="class_bam_tools_1_1_i_bam_i_o_device.html"> 27</a></span> <span class="keyword">class </span><a class="code" href="api__global_8h.html#a5e3652cae8b48c1ad174f0b06bbd06d0">API_EXPORT</a> <a class="code" href="class_bam_tools_1_1_i_bam_i_o_device.html">IBamIODevice</a> {</div><div class="line"><a name="l00028"></a><span class="lineno"> 28</span> </div><div class="line"><a name="l00029"></a><span class="lineno"> 29</span>  <span class="comment">// enums</span></div><div class="line"><a name="l00030"></a><span class="lineno"><a class="line" href="class_bam_tools_1_1_i_bam_i_o_device.html#a97309e79d2a827f02b748ebbfbe0363f"> 30</a></span>  <span class="keyword">public</span>: <span class="keyword">enum</span> <a class="code" href="class_bam_tools_1_1_i_bam_i_o_device.html#a97309e79d2a827f02b748ebbfbe0363f">OpenMode</a> { NotOpen = 0x0000</div><div class="line"><a name="l00031"></a><span class="lineno"><a class="line" href="class_bam_tools_1_1_i_bam_i_o_device.html#a97309e79d2a827f02b748ebbfbe0363fa645c01fab293cd9f7ece68482c37fb6c"> 31</a></span>  , ReadOnly = 0x0001</div><div class="line"><a name="l00032"></a><span class="lineno"><a class="line" href="class_bam_tools_1_1_i_bam_i_o_device.html#a97309e79d2a827f02b748ebbfbe0363fa2f19dae7f3a87fd2155346fb8906a717"> 32</a></span>  , WriteOnly = 0x0002</div><div class="line"><a name="l00033"></a><span class="lineno"><a class="line" href="class_bam_tools_1_1_i_bam_i_o_device.html#a97309e79d2a827f02b748ebbfbe0363fa0f63fd0c93bb14d075885e361750144f"> 33</a></span>  , ReadWrite = ReadOnly | WriteOnly</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> </div><div class="line"><a name="l00036"></a><span class="lineno"> 36</span>  <span class="comment">// ctor & dtor</span></div><div class="line"><a name="l00037"></a><span class="lineno"> 37</span>  <span class="keyword">public</span>:</div><div class="line"><a name="l00038"></a><span class="lineno"><a class="line" href="class_bam_tools_1_1_i_bam_i_o_device.html#acc675a3d613b2f03bfe1717548d648b2"> 38</a></span>  <span class="keyword">virtual</span> <a class="code" href="class_bam_tools_1_1_i_bam_i_o_device.html#acc675a3d613b2f03bfe1717548d648b2">~IBamIODevice</a>(<span class="keywordtype">void</span>) { }</div><div class="line"><a name="l00039"></a><span class="lineno"> 39</span> </div><div class="line"><a name="l00040"></a><span class="lineno"> 40</span>  <span class="comment">// IBamIODevice interface</span></div><div class="line"><a name="l00041"></a><span class="lineno"> 41</span>  <span class="keyword">public</span>:</div><div class="line"><a name="l00042"></a><span class="lineno"> 42</span> </div><div class="line"><a name="l00043"></a><span class="lineno"> 43</span>  <span class="comment">// TODO: add seek(pos, *from*)</span></div><div class="line"><a name="l00044"></a><span class="lineno"> 44</span> </div><div class="line"><a name="l00045"></a><span class="lineno"> 45</span>  <span class="comment">// pure virtuals</span></div><div class="line"><a name="l00046"></a><span class="lineno"> 46</span>  <span class="keyword">virtual</span> <span class="keywordtype">void</span> Close(<span class="keywordtype">void</span>) =0;</div><div class="line"><a name="l00047"></a><span class="lineno"> 47</span>  <span class="keyword">virtual</span> <span class="keywordtype">bool</span> IsRandomAccess(<span class="keywordtype">void</span>) <span class="keyword">const</span> =0;</div><div class="line"><a name="l00048"></a><span class="lineno"> 48</span>  <span class="keyword">virtual</span> <span class="keywordtype">bool</span> Open(<span class="keyword">const</span> <a class="code" href="class_bam_tools_1_1_i_bam_i_o_device.html#a97309e79d2a827f02b748ebbfbe0363f">OpenMode</a> mode) =0;</div><div class="line"><a name="l00049"></a><span class="lineno"> 49</span>  <span class="keyword">virtual</span> int64_t Read(<span class="keywordtype">char</span>* data, <span class="keyword">const</span> <span class="keywordtype">unsigned</span> <span class="keywordtype">int</span> numBytes) =0;</div><div class="line"><a name="l00050"></a><span class="lineno"> 50</span>  <span class="keyword">virtual</span> <span class="keywordtype">bool</span> Seek(<span class="keyword">const</span> int64_t& position, <span class="keyword">const</span> <span class="keywordtype">int</span> origin = SEEK_SET) =0;</div><div class="line"><a name="l00051"></a><span class="lineno"> 51</span>  <span class="keyword">virtual</span> int64_t Tell(<span class="keywordtype">void</span>) <span class="keyword">const</span> =0;</div><div class="line"><a name="l00052"></a><span class="lineno"> 52</span>  <span class="keyword">virtual</span> int64_t Write(<span class="keyword">const</span> <span class="keywordtype">char</span>* data, <span class="keyword">const</span> <span class="keywordtype">unsigned</span> <span class="keywordtype">int</span> numBytes) =0;</div><div class="line"><a name="l00053"></a><span class="lineno"> 53</span> </div><div class="line"><a name="l00054"></a><span class="lineno"> 54</span>  <span class="comment">// default implementation provided</span></div><div class="line"><a name="l00055"></a><span class="lineno"> 55</span>  <span class="keyword">virtual</span> std::string GetErrorString(<span class="keywordtype">void</span>);</div><div class="line"><a name="l00056"></a><span class="lineno"> 56</span>  <span class="keyword">virtual</span> <span class="keywordtype">bool</span> IsOpen(<span class="keywordtype">void</span>) <span class="keyword">const</span>;</div><div class="line"><a name="l00057"></a><span class="lineno"> 57</span>  <span class="keyword">virtual</span> <a class="code" href="class_bam_tools_1_1_i_bam_i_o_device.html#a97309e79d2a827f02b748ebbfbe0363f">OpenMode</a> Mode(<span class="keywordtype">void</span>) <span class="keyword">const</span>;</div><div class="line"><a name="l00058"></a><span class="lineno"> 58</span> </div><div class="line"><a name="l00059"></a><span class="lineno"> 59</span>  <span class="comment">// internal methods</span></div><div class="line"><a name="l00060"></a><span class="lineno"> 60</span>  <span class="keyword">protected</span>:</div><div class="line"><a name="l00061"></a><span class="lineno"> 61</span>  <a class="code" href="class_bam_tools_1_1_i_bam_i_o_device.html">IBamIODevice</a>(<span class="keywordtype">void</span>); <span class="comment">// hidden ctor</span></div><div class="line"><a name="l00062"></a><span class="lineno"> 62</span>  <span class="keywordtype">void</span> SetErrorString(<span class="keyword">const</span> std::string& where, <span class="keyword">const</span> std::string& what);</div><div class="line"><a name="l00063"></a><span class="lineno"> 63</span> </div><div class="line"><a name="l00064"></a><span class="lineno"> 64</span>  <span class="comment">// data members</span></div><div class="line"><a name="l00065"></a><span class="lineno"> 65</span>  <span class="keyword">protected</span>:</div><div class="line"><a name="l00066"></a><span class="lineno"><a class="line" href="class_bam_tools_1_1_i_bam_i_o_device.html#a56e09712e67ebbaf6e203fa13182bef4"> 66</a></span>  <a class="code" href="class_bam_tools_1_1_i_bam_i_o_device.html#a97309e79d2a827f02b748ebbfbe0363f">OpenMode</a> <a class="code" href="class_bam_tools_1_1_i_bam_i_o_device.html#a56e09712e67ebbaf6e203fa13182bef4">m_mode</a>;</div><div class="line"><a name="l00067"></a><span class="lineno"><a class="line" href="class_bam_tools_1_1_i_bam_i_o_device.html#a27212a1126cc9f0134539cb5e1288c0b"> 67</a></span>  std::string <a class="code" href="class_bam_tools_1_1_i_bam_i_o_device.html#a27212a1126cc9f0134539cb5e1288c0b">m_errorString</a>;</div><div class="line"><a name="l00068"></a><span class="lineno"> 68</span> };</div><div class="line"><a name="l00069"></a><span class="lineno"> 69</span> </div><div class="line"><a name="l00070"></a><span class="lineno"> 70</span> <span class="keyword">inline</span></div><div class="line"><a name="l00071"></a><span class="lineno"><a class="line" href="class_bam_tools_1_1_i_bam_i_o_device.html#a22e5bf5468d471a2cd6fcad376ef749f"> 71</a></span> <a class="code" href="class_bam_tools_1_1_i_bam_i_o_device.html#a22e5bf5468d471a2cd6fcad376ef749f">IBamIODevice::IBamIODevice</a>(<span class="keywordtype">void</span>)</div><div class="line"><a name="l00072"></a><span class="lineno"> 72</span>  : m_mode(<a class="code" href="class_bam_tools_1_1_i_bam_i_o_device.html">IBamIODevice</a>::NotOpen)</div><div class="line"><a name="l00073"></a><span class="lineno"> 73</span> { }</div><div class="line"><a name="l00074"></a><span class="lineno"> 74</span> </div><div class="line"><a name="l00075"></a><span class="lineno"> 75</span> <span class="keyword">inline</span></div><div class="line"><a name="l00076"></a><span class="lineno"><a class="line" href="class_bam_tools_1_1_i_bam_i_o_device.html#a6a4063478e55978799696e9af3d69e0d"> 76</a></span> std::string <a class="code" href="class_bam_tools_1_1_i_bam_i_o_device.html#a6a4063478e55978799696e9af3d69e0d">IBamIODevice::GetErrorString</a>(<span class="keywordtype">void</span>) {</div><div class="line"><a name="l00077"></a><span class="lineno"> 77</span>  <span class="keywordflow">return</span> <a class="code" href="class_bam_tools_1_1_i_bam_i_o_device.html#a27212a1126cc9f0134539cb5e1288c0b">m_errorString</a>;</div><div class="line"><a name="l00078"></a><span class="lineno"> 78</span> }</div><div class="line"><a name="l00079"></a><span class="lineno"> 79</span> </div><div class="line"><a name="l00080"></a><span class="lineno"> 80</span> <span class="keyword">inline</span></div><div class="line"><a name="l00081"></a><span class="lineno"><a class="line" href="class_bam_tools_1_1_i_bam_i_o_device.html#ac43eb0a0ba3558664837452cff379796"> 81</a></span> <span class="keywordtype">bool</span> <a class="code" href="class_bam_tools_1_1_i_bam_i_o_device.html#ac43eb0a0ba3558664837452cff379796">IBamIODevice::IsOpen</a>(<span class="keywordtype">void</span>)<span class="keyword"> const </span>{</div><div class="line"><a name="l00082"></a><span class="lineno"> 82</span>  <span class="keywordflow">return</span> ( <a class="code" href="class_bam_tools_1_1_i_bam_i_o_device.html#a56e09712e67ebbaf6e203fa13182bef4">m_mode</a> != <a class="code" href="class_bam_tools_1_1_i_bam_i_o_device.html#a97309e79d2a827f02b748ebbfbe0363fa33dd1b7df3b89980411a7cfd3b9385fb">IBamIODevice::NotOpen</a> );</div><div class="line"><a name="l00083"></a><span class="lineno"> 83</span> }</div><div class="line"><a name="l00084"></a><span class="lineno"> 84</span> </div><div class="line"><a name="l00085"></a><span class="lineno"> 85</span> <span class="keyword">inline</span></div><div class="line"><a name="l00086"></a><span class="lineno"><a class="line" href="class_bam_tools_1_1_i_bam_i_o_device.html#acfccb4aa90ae284cb6b2bb5fba803c05"> 86</a></span> <a class="code" href="class_bam_tools_1_1_i_bam_i_o_device.html#a97309e79d2a827f02b748ebbfbe0363f">IBamIODevice::OpenMode</a> <a class="code" href="class_bam_tools_1_1_i_bam_i_o_device.html#acfccb4aa90ae284cb6b2bb5fba803c05">IBamIODevice::Mode</a>(<span class="keywordtype">void</span>)<span class="keyword"> const </span>{</div><div class="line"><a name="l00087"></a><span class="lineno"> 87</span>  <span class="keywordflow">return</span> <a class="code" href="class_bam_tools_1_1_i_bam_i_o_device.html#a56e09712e67ebbaf6e203fa13182bef4">m_mode</a>;</div><div class="line"><a name="l00088"></a><span class="lineno"> 88</span> }</div><div class="line"><a name="l00089"></a><span class="lineno"> 89</span> </div><div class="line"><a name="l00090"></a><span class="lineno"> 90</span> <span class="keyword">inline</span></div><div class="line"><a name="l00091"></a><span class="lineno"><a class="line" href="class_bam_tools_1_1_i_bam_i_o_device.html#a445988198f0856a3b2c49fcc1b21aa75"> 91</a></span> <span class="keywordtype">void</span> <a class="code" href="class_bam_tools_1_1_i_bam_i_o_device.html#a445988198f0856a3b2c49fcc1b21aa75">IBamIODevice::SetErrorString</a>(<span class="keyword">const</span> std::string& where, <span class="keyword">const</span> std::string& what) {</div><div class="line"><a name="l00092"></a><span class="lineno"> 92</span>  <span class="keyword">static</span> <span class="keyword">const</span> std::string SEPARATOR = <span class="stringliteral">": "</span>;</div><div class="line"><a name="l00093"></a><span class="lineno"> 93</span>  <a class="code" href="class_bam_tools_1_1_i_bam_i_o_device.html#a27212a1126cc9f0134539cb5e1288c0b">m_errorString</a> = where + SEPARATOR + what;</div><div class="line"><a name="l00094"></a><span class="lineno"> 94</span> }</div><div class="line"><a name="l00095"></a><span class="lineno"> 95</span> </div><div class="line"><a name="l00096"></a><span class="lineno"> 96</span> } <span class="comment">// namespace BamTools</span></div><div class="line"><a name="l00097"></a><span class="lineno"> 97</span> </div><div class="line"><a name="l00098"></a><span class="lineno"> 98</span> <span class="preprocessor">#endif // IBAMIODEVICE_H</span></div><div class="ttc" id="class_bam_tools_1_1_i_bam_i_o_device_html_a97309e79d2a827f02b748ebbfbe0363f"><div class="ttname"><a href="class_bam_tools_1_1_i_bam_i_o_device.html#a97309e79d2a827f02b748ebbfbe0363f">BamTools::IBamIODevice::OpenMode</a></div><div class="ttdeci">OpenMode</div><div class="ttdef"><b>Definition:</b> IBamIODevice.h:30</div></div>
<div class="ttc" id="class_bam_tools_1_1_i_bam_i_o_device_html"><div class="ttname"><a href="class_bam_tools_1_1_i_bam_i_o_device.html">BamTools::IBamIODevice</a></div><div class="ttdef"><b>Definition:</b> IBamIODevice.h:27</div></div>
<div class="ttc" id="class_bam_tools_1_1_i_bam_i_o_device_html_acfccb4aa90ae284cb6b2bb5fba803c05"><div class="ttname"><a href="class_bam_tools_1_1_i_bam_i_o_device.html#acfccb4aa90ae284cb6b2bb5fba803c05">BamTools::IBamIODevice::Mode</a></div><div class="ttdeci">virtual OpenMode Mode(void) const</div><div class="ttdef"><b>Definition:</b> IBamIODevice.h:86</div></div>
<div class="ttc" id="class_bam_tools_1_1_i_bam_i_o_device_html_a445988198f0856a3b2c49fcc1b21aa75"><div class="ttname"><a href="class_bam_tools_1_1_i_bam_i_o_device.html#a445988198f0856a3b2c49fcc1b21aa75">BamTools::IBamIODevice::SetErrorString</a></div><div class="ttdeci">void SetErrorString(const std::string &where, const std::string &what)</div><div class="ttdef"><b>Definition:</b> IBamIODevice.h:91</div></div>
<div class="ttc" id="class_bam_tools_1_1_i_bam_i_o_device_html_a22e5bf5468d471a2cd6fcad376ef749f"><div class="ttname"><a href="class_bam_tools_1_1_i_bam_i_o_device.html#a22e5bf5468d471a2cd6fcad376ef749f">BamTools::IBamIODevice::IBamIODevice</a></div><div class="ttdeci">IBamIODevice(void)</div><div class="ttdef"><b>Definition:</b> IBamIODevice.h:71</div></div>
<div class="ttc" id="api__global_8h_html_a5e3652cae8b48c1ad174f0b06bbd06d0"><div class="ttname"><a href="api__global_8h.html#a5e3652cae8b48c1ad174f0b06bbd06d0">API_EXPORT</a></div><div class="ttdeci">#define API_EXPORT</div><div class="ttdef"><b>Definition:</b> api_global.h:18</div></div>
<div class="ttc" id="class_bam_tools_1_1_i_bam_i_o_device_html_acc675a3d613b2f03bfe1717548d648b2"><div class="ttname"><a href="class_bam_tools_1_1_i_bam_i_o_device.html#acc675a3d613b2f03bfe1717548d648b2">BamTools::IBamIODevice::~IBamIODevice</a></div><div class="ttdeci">virtual ~IBamIODevice(void)</div><div class="ttdef"><b>Definition:</b> IBamIODevice.h:38</div></div>
<div class="ttc" id="class_bam_tools_1_1_i_bam_i_o_device_html_ac43eb0a0ba3558664837452cff379796"><div class="ttname"><a href="class_bam_tools_1_1_i_bam_i_o_device.html#ac43eb0a0ba3558664837452cff379796">BamTools::IBamIODevice::IsOpen</a></div><div class="ttdeci">virtual bool IsOpen(void) const</div><div class="ttdef"><b>Definition:</b> IBamIODevice.h:81</div></div>
<div class="ttc" id="class_bam_tools_1_1_i_bam_i_o_device_html_a97309e79d2a827f02b748ebbfbe0363fa33dd1b7df3b89980411a7cfd3b9385fb"><div class="ttname"><a href="class_bam_tools_1_1_i_bam_i_o_device.html#a97309e79d2a827f02b748ebbfbe0363fa33dd1b7df3b89980411a7cfd3b9385fb">BamTools::IBamIODevice::NotOpen</a></div><div class="ttdef"><b>Definition:</b> IBamIODevice.h:30</div></div>
<div class="ttc" id="class_bam_tools_1_1_i_bam_i_o_device_html_a56e09712e67ebbaf6e203fa13182bef4"><div class="ttname"><a href="class_bam_tools_1_1_i_bam_i_o_device.html#a56e09712e67ebbaf6e203fa13182bef4">BamTools::IBamIODevice::m_mode</a></div><div class="ttdeci">OpenMode m_mode</div><div class="ttdef"><b>Definition:</b> IBamIODevice.h:66</div></div>
<div class="ttc" id="class_bam_tools_1_1_i_bam_i_o_device_html_a27212a1126cc9f0134539cb5e1288c0b"><div class="ttname"><a href="class_bam_tools_1_1_i_bam_i_o_device.html#a27212a1126cc9f0134539cb5e1288c0b">BamTools::IBamIODevice::m_errorString</a></div><div class="ttdeci">std::string m_errorString</div><div class="ttdef"><b>Definition:</b> IBamIODevice.h:67</div></div>
<div class="ttc" id="namespace_bam_tools_html"><div class="ttname"><a href="namespace_bam_tools.html">BamTools</a></div><div class="ttdoc">Contains all BamTools classes & methods. </div><div class="ttdef"><b>Definition:</b> Sort.h:24</div></div>
<div class="ttc" id="api__global_8h_html"><div class="ttname"><a href="api__global_8h.html">api_global.h</a></div></div>
<div class="ttc" id="class_bam_tools_1_1_i_bam_i_o_device_html_a6a4063478e55978799696e9af3d69e0d"><div class="ttname"><a href="class_bam_tools_1_1_i_bam_i_o_device.html#a6a4063478e55978799696e9af3d69e0d">BamTools::IBamIODevice::GetErrorString</a></div><div class="ttdeci">virtual std::string GetErrorString(void)</div><div class="ttdef"><b>Definition:</b> IBamIODevice.h:76</div></div>
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