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<!DOCTYPE html PUBLIC "-//W3C//DTD XHTML 1.0 Transitional//EN" "https://www.w3.org/TR/xhtml1/DTD/xhtml1-transitional.dtd">
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<div class="title">xsample08.cpp</div> </div>
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<p>Example on intervals and how to use it for layout calculation.As a use case this example uses genomics visualization for features mapped into genomic coordinates.</p>
<p>It is also illustartes vector model using coordinate ranges or feature vectors. Various properties of the initial model acn be dropped (sliced) to improve memory efficiency, better storage or network transfer.</p>
<p>This example does NOT do serialization of models (which is possible) for the clarity of the sample code.</p>
<dl class="section see"><dt>See also</dt><dd><a class="el" href="classbm_1_1bvector.html#aafb2ecaa1a55856533e6b4afbf788eae" title="Sets all bits in the specified closed interval [left,right] Interval must be inside the bvector's siz...">bm::bvector::set_range</a> </dd>
<dd>
<a class="el" href="classbm_1_1bvector.html#a530f12c9a00799ecbe9abd276a7ae619" title="Returns true if any bits in the range are 1s (non-empty interval) Function uses closed interval [left...">bm::bvector::any_range</a> </dd>
<dd>
<a class="el" href="classbm_1_1bvector.html#ab7978570375ae288a6893d7b4d673769" title="Copy all bits in the specified closed interval [left,right].">bm::bvector::copy_range</a> </dd>
<dd>
<a class="el" href="classbm_1_1interval__enumerator.html" title="forward iterator class to traverse bit-vector as ranges">bm::interval_enumerator</a> </dd>
<dd>
<a class="el" href="classbm_1_1rsc__sparse__vector.html" title="Rank-Select compressed sparse vector.">bm::rsc_sparse_vector</a> </dd>
<dd>
<a class="el" href="classbm_1_1rsc__sparse__vector.html#ad6ff45327aaf9c9494f838071e563726" title="copy range of values from another sparse vector">bm::rsc_sparse_vector::copy_range</a> </dd>
<dd>
<a class="el" href="group__bvintervals.html#gaa184975ff6e9b314ab559f132e730880" title="Reverse find index of first 1 bit gap (01110) starting from position Reverse scan for the first 1 in ...">bm::find_interval_start</a> </dd>
<dd>
<a class="el" href="group__bvintervals.html#ga41642899622fcb337ef94b6861f40f92" title="Reverse find index of first 1 bit gap (01110) starting from position Reverse scan for the first 1 in ...">bm::find_interval_end</a></dd>
<dd>
<a class="el" href="sample22_8cpp.html" title="Example: bvector<> - ranges and intervals functions.">sample22.cpp</a> </dd>
<dd>
<a class="el" href="sample23_8cpp.html" title="Example: interval_enumerator<> - interator class for intervals.">sample23.cpp</a> </dd>
<dd>
<a class="el" href="group__bvintervals.html" title="Algorithms and iterators for bit ranges and intervals.">Algorithms for bit intervals</a></dd></dl>
<div class="fragment"><div class="line"><span class="comment">/*</span></div>
<div class="line"><span class="comment">Copyright(c) 2002-2017 Anatoliy Kuznetsov(anatoliy_kuznetsov at yahoo.com)</span></div>
<div class="line"><span class="comment"></span> </div>
<div class="line"><span class="comment">Licensed under the Apache License, Version 2.0 (the "License");</span></div>
<div class="line"><span class="comment">you may not use this file except in compliance with the License.</span></div>
<div class="line"><span class="comment">You may obtain a copy of the License at</span></div>
<div class="line"><span class="comment"></span> </div>
<div class="line"><span class="comment"> http://www.apache.org/licenses/LICENSE-2.0</span></div>
<div class="line"><span class="comment"></span> </div>
<div class="line"><span class="comment">Unless required by applicable law or agreed to in writing, software</span></div>
<div class="line"><span class="comment">distributed under the License is distributed on an "AS IS" BASIS,</span></div>
<div class="line"><span class="comment">WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.</span></div>
<div class="line"><span class="comment">See the License for the specific language governing permissions and</span></div>
<div class="line"><span class="comment">limitations under the License.</span></div>
<div class="line"><span class="comment"></span> </div>
<div class="line"><span class="comment">For more information please visit: http://bitmagic.io</span></div>
<div class="line"><span class="comment">*/</span></div>
<div class="line"><span class="comment"></span> </div>
<div class="line"><span class="comment">/** \example xsample08.cpp</span></div>
<div class="line"><span class="comment"></span> </div>
<div class="line"><span class="comment"> Example on intervals and how to use it for layout calculation.</span></div>
<div class="line"><span class="comment"> As a use case this example uses genomics visualization for</span></div>
<div class="line"><span class="comment"> features mapped into genomic coordinates.</span></div>
<div class="line"><span class="comment"></span> </div>
<div class="line"><span class="comment"> It is also illustartes vector model using coordinate ranges</span></div>
<div class="line"><span class="comment"> or feature vectors. Various properties of the initial model acn be</span></div>
<div class="line"><span class="comment"> dropped (sliced) to improve memory efficiency, better storage</span></div>
<div class="line"><span class="comment"> or network transfer.</span></div>
<div class="line"><span class="comment"></span> </div>
<div class="line"><span class="comment"> This example does NOT do serialization of models (which is possible)</span></div>
<div class="line"><span class="comment"> for the clarity of the sample code.</span></div>
<div class="line"><span class="comment"></span> </div>
<div class="line"><span class="comment"> \sa bm::bvector::set_range</span></div>
<div class="line"><span class="comment"> \sa bm::bvector::any_range</span></div>
<div class="line"><span class="comment"> \sa bm::bvector::copy_range</span></div>
<div class="line"><span class="comment"> \sa bm::interval_enumerator</span></div>
<div class="line"><span class="comment"> \sa bm::rsc_sparse_vector</span></div>
<div class="line"><span class="comment"> \sa bm::rsc_sparse_vector::copy_range</span></div>
<div class="line"><span class="comment"> \sa bm::find_interval_start</span></div>
<div class="line"><span class="comment"> \sa bm::find_interval_end</span></div>
<div class="line"><span class="comment"></span> </div>
<div class="line"><span class="comment"> \sa sample22.cpp</span></div>
<div class="line"><span class="comment"> \sa sample23.cpp</span></div>
<div class="line"><span class="comment"> \sa bvintervals</span></div>
<div class="line"><span class="comment">*/</span></div>
<div class="line"><span class="comment"></span> </div>
<div class="line"><span class="comment">/*! \file sample23.cpp</span></div>
<div class="line"><span class="comment"> \brief Example: interval_enumerator<> - interator class for intervals</span></div>
<div class="line"><span class="comment">*/</span></div>
<div class="line"> </div>
<div class="line"><span class="preprocessor">#include <iostream></span></div>
<div class="line"><span class="preprocessor">#include <utility></span></div>
<div class="line"><span class="preprocessor">#include <vector></span></div>
<div class="line"><span class="preprocessor">#include <memory></span></div>
<div class="line"><span class="preprocessor">#include <cassert></span></div>
<div class="line"> </div>
<div class="line"><span class="preprocessor">#include "<a class="code" href="bm_8h.html">bm.h</a>"</span></div>
<div class="line"><span class="preprocessor">#include "<a class="code" href="bmintervals_8h.html">bmintervals.h</a>"</span></div>
<div class="line"><span class="preprocessor">#include "<a class="code" href="bmsparsevec__compr_8h.html">bmsparsevec_compr.h</a>"</span></div>
<div class="line"> </div>
<div class="line"><span class="keyword">using namespace </span>std;</div>
<div class="line"> </div>
<div class="line"><span class="keyword">typedef</span> <a name="_a0"></a><a class="code" href="classbm_1_1interval__enumerator.html">bm::interval_enumerator<bm::bvector<></a> > <a name="a1"></a><a class="code" href="xsample08_8cpp.html#a4818975b7767c5d423cbc0f181261cf4">interval_enumerator_type</a>;</div>
<div class="line"><span class="keyword">typedef</span> std::vector<std::unique_ptr<bm::bvector<> > > <a name="a2"></a><a class="code" href="xsample08_8cpp.html#af276e5a029922cc9fe0803b63a8eb363">layout_vector_type</a>;</div>
<div class="line"> </div>
<div class="line"><span class="keyword">typedef</span> <a name="_a3"></a><a class="code" href="classbm_1_1sparse__vector.html">bm::sparse_vector<unsigned char, bm::bvector<></a> > <a name="a4"></a><a class="code" href="xsample08_8cpp.html#a21ab0bc26ed51234f40ec4959e4e1868">sparse_vector_u8</a>;</div>
<div class="line"><span class="keyword">typedef</span> <a name="_a5"></a><a class="code" href="classbm_1_1rsc__sparse__vector.html">bm::rsc_sparse_vector<unsigned char, sparse_vector_u8></a> <a name="a6"></a><a class="code" href="xsample08_8cpp.html#a624e05d875c1dd02606ea289d96d9c62">rsc_vector_u8</a>;</div>
<div class="line"><span class="keyword">typedef</span> std::vector<std::unique_ptr<rsc_vector_u8> > <a name="a7"></a><a class="code" href="xsample08_8cpp.html#a570a10a183b6108efc4df372793d0563">starnds_vector_type</a>;</div>
<div class="line"> </div>
<div class="line"> </div>
<div class="line"><span class="comment">// -------------------------------------------------------------------</span></div>
<div class="line"><span class="comment"></span> </div>
<div class="line"><span class="comment">/// Data frame object, sued to buid succinct data model</span></div>
<div class="line"><span class="comment">///</span></div>
<div class="line"><span class="comment">///</span></div>
<div class="line"><span class="comment"></span><span class="keyword">struct </span><a name="_a8"></a><a class="code" href="structdata__model.html">data_model</a></div>
<div class="line">{<span class="comment"></span></div>
<div class="line"><span class="comment"> /// Optimize memory layoput, build index for faster read access</span></div>
<div class="line"><span class="comment"> ///</span></div>
<div class="line"><span class="comment"></span> <span class="keywordtype">void</span> optimize();</div>
<div class="line"> </div>
<div class="line"> <span class="keywordtype">void</span> add_layout(<span class="keywordtype">size_t</span> plane, <a name="_a9"></a><a class="code" href="classbm_1_1bvector.html">bm::bvector<></a>* bv);</div>
<div class="line"> <span class="keywordtype">void</span> add_strand(<span class="keywordtype">size_t</span> plane, <a class="code" href="classbm_1_1rsc__sparse__vector.html">rsc_vector_u8</a>* strand);</div>
<div class="line"> </div>
<div class="line"> <a class="code" href="xsample08_8cpp.html#af276e5a029922cc9fe0803b63a8eb363">layout_vector_type</a> layout_v; <span class="comment">///< layout vector</span></div>
<div class="line"><span class="comment"></span> <a class="code" href="xsample08_8cpp.html#a570a10a183b6108efc4df372793d0563">starnds_vector_type</a> strand_v; <span class="comment">///< strand planes vector</span></div>
<div class="line"><span class="comment"></span>};</div>
<div class="line"> </div>
<div class="line"><span class="keywordtype">void</span> <a name="a10"></a><a class="code" href="structdata__model.html#a0444be6631839b756ec5b9f16c5f0567">data_model::optimize</a>()</div>
<div class="line">{</div>
<div class="line"> <a name="a11"></a><a class="code" href="bm_8h.html#ad9736d9521d713fa5d48859aa720bfdd">BM_DECLARE_TEMP_BLOCK</a>(tb); <span class="comment">// explicit temp for faster optimization</span></div>
<div class="line"> <span class="keywordflow">for</span> (<span class="keywordtype">size_t</span> i = 0; i < layout_v.size(); ++i)</div>
<div class="line"> {</div>
<div class="line"> <span class="keyword">auto</span> bv = layout_v[i].get();</div>
<div class="line"> <span class="keywordflow">if</span> (bv)</div>
<div class="line"> bv->optimize(tb); <span class="comment">// memory optimization</span></div>
<div class="line"> } <span class="comment">// for i</span></div>
<div class="line"> <span class="keywordflow">for</span> (<span class="keywordtype">size_t</span> i = 0; i < strand_v.size(); ++i)</div>
<div class="line"> {</div>
<div class="line"> <span class="keyword">auto</span> strand_plane = strand_v[i].get();</div>
<div class="line"> <span class="keywordflow">if</span> (strand_plane)</div>
<div class="line"> {</div>
<div class="line"> strand_plane->optimize(tb);</div>
<div class="line"> strand_plane->sync(); <span class="comment">// build rank-select idx (faster read access)</span></div>
<div class="line"> }</div>
<div class="line"> } <span class="comment">// for i</span></div>
<div class="line">}</div>
<div class="line"> </div>
<div class="line"><span class="keywordtype">void</span> <a name="a12"></a><a class="code" href="structdata__model.html#a5c626772440999a94b6f3ce851bc916f">data_model::add_layout</a>(<span class="keywordtype">size_t</span> plane, <a class="code" href="classbm_1_1bvector.html">bm::bvector<></a>* bv)</div>
<div class="line">{</div>
<div class="line"> unique_ptr<bm::bvector<> > ap(bv);</div>
<div class="line"> <span class="keywordflow">if</span> (layout_v.size() == plane) <span class="comment">// push back requested</span></div>
<div class="line"> {</div>
<div class="line"> layout_v.emplace_back(move(ap));</div>
<div class="line"> }</div>
<div class="line"> <span class="keywordflow">else</span></div>
<div class="line"> {</div>
<div class="line"> <span class="keywordflow">while</span> (layout_v.size() < plane) <span class="comment">// this is crude resize() but it would do</span></div>
<div class="line"> layout_v.emplace_back(<span class="keyword">new</span> <a class="code" href="classbm_1_1bvector.html">bm::bvector<></a>(<a name="a13"></a><a class="code" href="group__bvector.html#ggad0b87b3b7292383a864d27feaf1c9effa7fe09d1d7c62a813db922c396c0cbc9c">bm::BM_GAP</a>));</div>
<div class="line"> layout_v[plane] = std::move(ap);</div>
<div class="line"> }</div>
<div class="line">}</div>
<div class="line"> </div>
<div class="line"><span class="keywordtype">void</span> <a name="a14"></a><a class="code" href="structdata__model.html#a2b5714a796e1485b7ea503d6c9f8ba02">data_model::add_strand</a>(<span class="keywordtype">size_t</span> plane, <a class="code" href="classbm_1_1rsc__sparse__vector.html">rsc_vector_u8</a>* strand)</div>
<div class="line">{</div>
<div class="line"> unique_ptr<rsc_vector_u8 > ap(strand);</div>
<div class="line"> <span class="keywordflow">if</span> (strand_v.size() == plane) <span class="comment">// push back requested</span></div>
<div class="line"> {</div>
<div class="line"> strand_v.emplace_back(move(ap));</div>
<div class="line"> }</div>
<div class="line"> <span class="keywordflow">else</span></div>
<div class="line"> {</div>
<div class="line"> <span class="keywordflow">while</span> (strand_v.size() < plane) <span class="comment">// this is crude resize() but it would do</span></div>
<div class="line"> strand_v.emplace_back(<span class="keyword">new</span> <a class="code" href="xsample08_8cpp.html#a624e05d875c1dd02606ea289d96d9c62">rsc_vector_u8</a>());</div>
<div class="line"> strand_v[plane] = std::move(ap);</div>
<div class="line"> }</div>
<div class="line">}</div>
<div class="line"> </div>
<div class="line"> </div>
<div class="line"><span class="comment">// -------------------------------------------------------------------</span></div>
<div class="line"> </div>
<div class="line"><span class="keywordtype">void</span> <a name="a15"></a><a class="code" href="xsample08_8cpp.html#a94126954222ad24c55587827067e134d">set_feature_strand</a>(<a class="code" href="structdata__model.html">data_model</a>& dm, <span class="keywordtype">size_t</span> plane,</div>
<div class="line"> <a class="code" href="classbm_1_1bvector.html#a405dd9ed048c935c84a5086ec8ba3649">bm::bvector<>::size_type</a> pos,</div>
<div class="line"> <span class="keywordtype">unsigned</span> <span class="keywordtype">char</span> strand)</div>
<div class="line">{</div>
<div class="line"> <span class="keywordflow">if</span> (!strand)</div>
<div class="line"> <span class="keywordflow">return</span>;</div>
<div class="line"> <span class="keywordflow">while</span> (dm.<a name="a16"></a><a class="code" href="structdata__model.html#ae98a6571059d2235083b08aca3957cfc">strand_v</a>.size() <= plane) <span class="comment">// add planes</span></div>
<div class="line"> {</div>
<div class="line"> std::unique_ptr<rsc_vector_u8> p2(<span class="keyword">new</span> <a class="code" href="xsample08_8cpp.html#a624e05d875c1dd02606ea289d96d9c62">rsc_vector_u8</a>());</div>
<div class="line"> dm.<a class="code" href="structdata__model.html#ae98a6571059d2235083b08aca3957cfc">strand_v</a>.emplace_back(move(p2));</div>
<div class="line"> }</div>
<div class="line"> </div>
<div class="line"> <a class="code" href="classbm_1_1rsc__sparse__vector.html">rsc_vector_u8</a>* strand_plane = dm.<a class="code" href="structdata__model.html#ae98a6571059d2235083b08aca3957cfc">strand_v</a>[plane].get();</div>
<div class="line"> <span class="keywordflow">if</span> (!strand_plane)</div>
<div class="line"> {</div>
<div class="line"> strand_plane = <span class="keyword">new</span> <a class="code" href="xsample08_8cpp.html#a624e05d875c1dd02606ea289d96d9c62">rsc_vector_u8</a>();</div>
<div class="line"> dm.<a class="code" href="structdata__model.html#ae98a6571059d2235083b08aca3957cfc">strand_v</a>[plane] = unique_ptr<rsc_vector_u8 >(strand_plane);</div>
<div class="line"> }</div>
<div class="line"> assert(strand_plane-><a name="a17"></a><a class="code" href="classbm_1_1rsc__sparse__vector.html#aa8e0eeff8947aac3899ee79d5c040ca9">is_null</a>(pos));</div>
<div class="line"> strand_plane-><a name="a18"></a><a class="code" href="classbm_1_1rsc__sparse__vector.html#a3fcda99085ab1d9f9cca1a6ce48f543e">set</a>(pos, strand);</div>
<div class="line">}</div>
<div class="line"><span class="comment"></span> </div>
<div class="line"><span class="comment">/// Register new object in the data model: [start..end] + strand</span></div>
<div class="line"><span class="comment">///</span></div>
<div class="line"><span class="comment"></span><span class="keywordtype">void</span> <a name="a19"></a><a class="code" href="xsample08_8cpp.html#a704b4ac4464e1c71312fb580b441a0be">add_object</a>(<a class="code" href="structdata__model.html">data_model</a>& dm,</div>
<div class="line"> <span class="keywordtype">unsigned</span> start, <span class="keywordtype">unsigned</span> end,</div>
<div class="line"> <span class="keywordtype">unsigned</span> <span class="keywordtype">char</span> strand)</div>
<div class="line">{</div>
<div class="line"> assert(start <= end);</div>
<div class="line"> </div>
<div class="line"> <a class="code" href="classbm_1_1bvector.html">bm::bvector<></a>* bv; <span class="comment">// layout plane vector</span></div>
<div class="line"> </div>
<div class="line"> <span class="keywordflow">for</span> (<span class="keywordtype">size_t</span> i = 0; i < dm.<a name="a20"></a><a class="code" href="structdata__model.html#ad02501c19c47ee7f99a74a7cd8a6f2da">layout_v</a>.size(); ++i)</div>
<div class="line"> {</div>
<div class="line"> bv = dm.<a class="code" href="structdata__model.html#ad02501c19c47ee7f99a74a7cd8a6f2da">layout_v</a>[i].get();</div>
<div class="line"> <span class="keywordflow">if</span> (!bv)</div>
<div class="line"> {</div>
<div class="line"> bv = <span class="keyword">new</span> <a class="code" href="classbm_1_1bvector.html">bm::bvector<></a>(<a class="code" href="group__bvector.html#ggad0b87b3b7292383a864d27feaf1c9effa7fe09d1d7c62a813db922c396c0cbc9c">bm::BM_GAP</a>);</div>
<div class="line"> dm.<a class="code" href="structdata__model.html#ad02501c19c47ee7f99a74a7cd8a6f2da">layout_v</a>[i] = unique_ptr<bm::bvector<> >(bv);</div>
<div class="line"> <span class="comment">// bv just created (empty) no need to do range check</span></div>
<div class="line"> bv-><a name="a21"></a><a class="code" href="classbm_1_1bvector.html#aafb2ecaa1a55856533e6b4afbf788eae">set_range</a>(start, end);</div>
<div class="line"> <a class="code" href="xsample08_8cpp.html#a94126954222ad24c55587827067e134d">set_feature_strand</a>(dm, i, start, strand);</div>
<div class="line"> </div>
<div class="line"> <span class="keywordflow">return</span>;</div>
<div class="line"> }</div>
<div class="line"> <span class="keywordflow">if</span> (!bv-><a name="a22"></a><a class="code" href="classbm_1_1bvector.html#a530f12c9a00799ecbe9abd276a7ae619">any_range</a>(start, end)) <span class="comment">// check if layout space is not used</span></div>
<div class="line"> {</div>
<div class="line"> bv-><a class="code" href="classbm_1_1bvector.html#aafb2ecaa1a55856533e6b4afbf788eae">set_range</a>(start, end); <span class="comment">// add [start..end] coordinates</span></div>
<div class="line"> <span class="comment">// set strand at the start of feature</span></div>
<div class="line"> <a class="code" href="xsample08_8cpp.html#a94126954222ad24c55587827067e134d">set_feature_strand</a>(dm, i, start, strand);</div>
<div class="line"> </div>
<div class="line"> <span class="keywordflow">return</span>;</div>
<div class="line"> }</div>
<div class="line"> } <span class="comment">// for i</span></div>
<div class="line"> </div>
<div class="line"> <span class="comment">// not found, make new plane</span></div>
<div class="line"> <span class="comment">//</span></div>
<div class="line"> bv = <span class="keyword">new</span> <a class="code" href="classbm_1_1bvector.html">bm::bvector<></a>(<a class="code" href="group__bvector.html#ggad0b87b3b7292383a864d27feaf1c9effa7fe09d1d7c62a813db922c396c0cbc9c">bm::BM_GAP</a>);</div>
<div class="line"> dm.<a class="code" href="structdata__model.html#ad02501c19c47ee7f99a74a7cd8a6f2da">layout_v</a>.emplace_back(std::unique_ptr<<a class="code" href="classbm_1_1bvector.html">bm::bvector<></a> >(bv));</div>
<div class="line"> bv-><a class="code" href="classbm_1_1bvector.html#aafb2ecaa1a55856533e6b4afbf788eae">set_range</a>(start, end);</div>
<div class="line"> <a class="code" href="xsample08_8cpp.html#a94126954222ad24c55587827067e134d">set_feature_strand</a>(dm, dm.<a class="code" href="structdata__model.html#ad02501c19c47ee7f99a74a7cd8a6f2da">layout_v</a>.size()-1, start, strand);</div>
<div class="line">}</div>
<div class="line"><span class="comment"></span> </div>
<div class="line"><span class="comment">/// Data model splicer</span></div>
<div class="line"><span class="comment">///</span></div>
<div class="line"><span class="comment"></span> </div>
<div class="line"><span class="keywordtype">void</span> <a name="a23"></a><a class="code" href="xsample08_8cpp.html#a6dc270468776be32b200c6722489c91b">splice_model</a>(<a class="code" href="structdata__model.html">data_model</a>& dm_target, <span class="keyword">const</span> <a class="code" href="structdata__model.html">data_model</a>& dm,</div>
<div class="line"> <a class="code" href="classbm_1_1bvector.html#a405dd9ed048c935c84a5086ec8ba3649">bm::bvector<>::size_type</a> start,</div>
<div class="line"> <a class="code" href="classbm_1_1bvector.html#a405dd9ed048c935c84a5086ec8ba3649">bm::bvector<>::size_type</a> end,</div>
<div class="line"> <span class="keywordtype">bool</span> copy_strands)</div>
<div class="line">{</div>
<div class="line"> <span class="keyword">const</span> <a class="code" href="classbm_1_1bvector.html">bm::bvector<></a>* bv; <span class="comment">// layout</span></div>
<div class="line"> <span class="keyword">const</span> <a class="code" href="classbm_1_1rsc__sparse__vector.html">rsc_vector_u8</a>* strand_plane;</div>
<div class="line"> </div>
<div class="line"> <span class="keywordtype">size_t</span> t_plane = 0;</div>
<div class="line"> <span class="keywordflow">for</span> (<span class="keywordtype">size_t</span> i = 0; i < dm.<a class="code" href="structdata__model.html#ad02501c19c47ee7f99a74a7cd8a6f2da">layout_v</a>.size(); ++i)</div>
<div class="line"> {</div>
<div class="line"> bv = dm.<a class="code" href="structdata__model.html#ad02501c19c47ee7f99a74a7cd8a6f2da">layout_v</a>[i].get();</div>
<div class="line"> <span class="keywordflow">if</span> (bv)</div>
<div class="line"> {</div>
<div class="line"> <a class="code" href="classbm_1_1bvector.html#a405dd9ed048c935c84a5086ec8ba3649">bm::bvector<>::size_type</a> start_pos;</div>
<div class="line"> <a class="code" href="classbm_1_1bvector.html#a405dd9ed048c935c84a5086ec8ba3649">bm::bvector<>::size_type</a> end_pos;</div>
<div class="line"> </div>
<div class="line"> <span class="keywordtype">bool</span> found = <a name="a24"></a><a class="code" href="group__bvintervals.html#gaa184975ff6e9b314ab559f132e730880">bm::find_interval_start</a>(*bv, start, start_pos);</div>
<div class="line"> <span class="keywordflow">if</span> (!found)</div>
<div class="line"> start_pos = start;</div>
<div class="line"> found = <a name="a25"></a><a class="code" href="group__bvintervals.html#ga41642899622fcb337ef94b6861f40f92">bm::find_interval_end</a>(*bv, end, end_pos);</div>
<div class="line"> <span class="keywordflow">if</span> (!found)</div>
<div class="line"> end_pos = end;</div>
<div class="line"> </div>
<div class="line"> unique_ptr<bm::bvector<>> bv_ptr(<span class="keyword">new</span> <a class="code" href="classbm_1_1bvector.html">bm::bvector<></a>(<a class="code" href="group__bvector.html#ggad0b87b3b7292383a864d27feaf1c9effa7fe09d1d7c62a813db922c396c0cbc9c">bm::BM_GAP</a>));</div>
<div class="line"> bv_ptr->copy_range(*bv, start_pos, end_pos);</div>
<div class="line"> <span class="keywordflow">if</span> (bv_ptr->any()) <span class="comment">// copy range may have ended as empty</span></div>
<div class="line"> {</div>
<div class="line"> dm_target.<a class="code" href="structdata__model.html#a5c626772440999a94b6f3ce851bc916f">add_layout</a>(t_plane, bv_ptr.release());</div>
<div class="line"> </div>
<div class="line"> <span class="comment">// slice the strands plane (if requested)</span></div>
<div class="line"> <span class="comment">//</span></div>
<div class="line"> <span class="keywordflow">if</span> (copy_strands)</div>
<div class="line"> {</div>
<div class="line"> <span class="keywordflow">if</span> (i < dm.<a class="code" href="structdata__model.html#ae98a6571059d2235083b08aca3957cfc">strand_v</a>.size())</div>
<div class="line"> {</div>
<div class="line"> strand_plane = dm.<a class="code" href="structdata__model.html#ae98a6571059d2235083b08aca3957cfc">strand_v</a>[i].get();</div>
<div class="line"> <span class="keywordflow">if</span> (strand_plane)</div>
<div class="line"> {</div>
<div class="line"> unique_ptr<rsc_vector_u8> strand_ptr(<span class="keyword">new</span> <a class="code" href="xsample08_8cpp.html#a624e05d875c1dd02606ea289d96d9c62">rsc_vector_u8</a>());</div>
<div class="line"> strand_ptr->copy_range(*strand_plane, start_pos, end_pos);</div>
<div class="line"> dm_target.<a class="code" href="structdata__model.html#a2b5714a796e1485b7ea503d6c9f8ba02">add_strand</a>(t_plane, strand_ptr.release());</div>
<div class="line"> }</div>
<div class="line"> }</div>
<div class="line"> }</div>
<div class="line"> ++t_plane;</div>
<div class="line"> } <span class="comment">// if any()</span></div>
<div class="line"> </div>
<div class="line"> } <span class="comment">// if bv</span></div>
<div class="line"> } <span class="comment">// for i</span></div>
<div class="line"> </div>
<div class="line">}</div>
<div class="line"> </div>
<div class="line"><span class="comment"></span> </div>
<div class="line"><span class="comment">/// This is ASCII art "renderer" for the data model.</span></div>
<div class="line"><span class="comment">/// illustrates how to manipulate succinct data model to create graphics</span></div>
<div class="line"><span class="comment">///</span></div>
<div class="line"><span class="comment"></span><span class="keywordtype">void</span> <a name="a26"></a><a class="code" href="xsample08_8cpp.html#af5053305a6d00802a606429f4cceaa9c">print_model</a>(<span class="keyword">const</span> <a class="code" href="structdata__model.html">data_model</a>& dm)</div>
<div class="line">{</div>
<div class="line"> <span class="keyword">const</span> <a class="code" href="classbm_1_1bvector.html">bm::bvector<></a>* bv; <span class="comment">// layout</span></div>
<div class="line"> <span class="keyword">const</span> <a class="code" href="classbm_1_1rsc__sparse__vector.html">rsc_vector_u8</a>* strand_plane;</div>
<div class="line"> </div>
<div class="line"> <span class="comment">// Sequence on top is for purely decorative purposes</span></div>
<div class="line"> cout <<</div>
<div class="line"> <span class="stringliteral">"-------------------------------------------------------------------------"</span></div>
<div class="line"> << endl <<</div>
<div class="line"> <span class="stringliteral">"ATGTTAGCCCGCGCATATTATATATGTAGCGTATTAAGCGDGGAGATTACCCTTGCATTAGGTTANNNNNNNN"</span></div>
<div class="line"> << endl <<</div>
<div class="line"> <span class="stringliteral">"-------------------------------------------------------------------------"</span></div>
<div class="line"> << endl;</div>
<div class="line"> </div>
<div class="line"> <span class="keywordflow">for</span> (<span class="keywordtype">size_t</span> i = 0; i < dm.<a class="code" href="structdata__model.html#ad02501c19c47ee7f99a74a7cd8a6f2da">layout_v</a>.size(); ++i)</div>
<div class="line"> {</div>
<div class="line"> bv = dm.<a class="code" href="structdata__model.html#ad02501c19c47ee7f99a74a7cd8a6f2da">layout_v</a>[i].get();</div>
<div class="line"> <span class="keywordflow">if</span> (bv)</div>
<div class="line"> {</div>
<div class="line"> strand_plane = i < dm.<a class="code" href="structdata__model.html#ae98a6571059d2235083b08aca3957cfc">strand_v</a>.size() ? dm.<a class="code" href="structdata__model.html#ae98a6571059d2235083b08aca3957cfc">strand_v</a>[i].get() : <span class="keyword">nullptr</span>;</div>
<div class="line"> <a class="code" href="classbm_1_1interval__enumerator.html">interval_enumerator_type</a> ien(*bv);</div>
<div class="line"> <span class="keywordflow">if</span> (ien.valid())</div>
<div class="line"> {</div>
<div class="line"> <a class="code" href="classbm_1_1bvector.html#a405dd9ed048c935c84a5086ec8ba3649">bm::bvector<>::size_type</a> spaces = 0;</div>
<div class="line"> <span class="keywordflow">do</span></div>
<div class="line"> {</div>
<div class="line"> <span class="keyword">auto</span> st = ien.start(); <span class="keyword">auto</span> end = ien.<a name="a27"></a><a class="code" href="classbm_1_1bvector.html#a937cd13482984f234a5d94cc638c22b5">end</a>();</div>
<div class="line"> <span class="keywordtype">char</span> ch_strand = <span class="charliteral">'?'</span>;</div>
<div class="line"> <span class="keywordflow">if</span> (strand_plane)</div>
<div class="line"> {</div>
<div class="line"> <span class="keyword">auto</span> strand = strand_plane-><a name="a28"></a><a class="code" href="classbm_1_1rsc__sparse__vector.html#a90d532ba181599d75564153bc71a84fa">get</a>(st);</div>
<div class="line"> <span class="keywordflow">switch</span> (strand)</div>
<div class="line"> {</div>
<div class="line"> <span class="keywordflow">case</span> 0: ch_strand = <span class="charliteral">'>'</span>; <span class="keywordflow">break</span>; <span class="comment">// positive</span></div>
<div class="line"> <span class="keywordflow">case</span> 1: ch_strand = <span class="charliteral">'<'</span>; <span class="keywordflow">break</span>; <span class="comment">// negative</span></div>
<div class="line"> <span class="keywordflow">default</span>: <span class="keywordflow">break</span>; <span class="comment">// unknown strand</span></div>
<div class="line"> }</div>
<div class="line"> }</div>
<div class="line"> <span class="keywordflow">for</span> (; spaces < st; ++spaces)</div>
<div class="line"> cout << <span class="stringliteral">" "</span>;</div>
<div class="line"> <span class="keywordflow">for</span> (<span class="keywordtype">bool</span> first = <span class="keyword">true</span>; st <= end; ++st, first = <span class="keyword">false</span>)</div>
<div class="line"> {</div>
<div class="line"> <span class="keywordflow">if</span> (st == end)</div>
<div class="line"> cout << ch_strand;</div>
<div class="line"> <span class="keywordflow">else</span></div>
<div class="line"> cout << (first ? ch_strand : <span class="charliteral">'.'</span>);</div>
<div class="line"> } <span class="comment">// for</span></div>
<div class="line"> spaces = end+1;</div>
<div class="line"> } <span class="keywordflow">while</span> (ien.advance());</div>
<div class="line"> cout << endl;</div>
<div class="line"> }</div>
<div class="line"> }</div>
<div class="line"> } <span class="comment">// for</span></div>
<div class="line">}</div>
<div class="line"> </div>
<div class="line"><span class="keyword">enum</span> <a class="code" href="xsample08_8cpp.html#a6aeede226b1f5324cd2f58cbc64c38c9">Strand</a> { <a name="a29"></a><a class="code" href="xsample08_8cpp.html#a6aeede226b1f5324cd2f58cbc64c38c9af3e33603bf389e5b337ee5bdbc9558b9">positive</a>=0, <a name="a30"></a><a class="code" href="xsample08_8cpp.html#a6aeede226b1f5324cd2f58cbc64c38c9a7b1174d620ccd8d2a049d8440aa1fc4d">negative</a>=1, <a name="a31"></a><a class="code" href="xsample08_8cpp.html#a6aeede226b1f5324cd2f58cbc64c38c9a5b9f6d065e6e98483b3d3ed01f4f6cbe">unknown</a>=2 };</div>
<div class="line"> </div>
<div class="line"> </div>
<div class="line"> </div>
<div class="line"><span class="keywordtype">int</span> <a name="a32"></a><a class="code" href="xsample08_8cpp.html#a840291bc02cba5474a4cb46a9b9566fe">main</a>(<span class="keywordtype">void</span>)</div>
<div class="line">{</div>
<div class="line"> <span class="keywordflow">try</span></div>
<div class="line"> {</div>
<div class="line"> <a class="code" href="structdata__model.html">data_model</a> dm;</div>
<div class="line"> </div>
<div class="line"> <span class="comment">// build the data model using succinct vectors</span></div>
<div class="line"> <span class="comment">//</span></div>
<div class="line"> <a class="code" href="xsample08_8cpp.html#a704b4ac4464e1c71312fb580b441a0be">add_object</a>(dm, 0, 0, <a class="code" href="xsample08_8cpp.html#a6aeede226b1f5324cd2f58cbc64c38c9a7b1174d620ccd8d2a049d8440aa1fc4d">negative</a>);</div>
<div class="line"> <a class="code" href="xsample08_8cpp.html#a704b4ac4464e1c71312fb580b441a0be">add_object</a>(dm, 5, 10, <a class="code" href="xsample08_8cpp.html#a6aeede226b1f5324cd2f58cbc64c38c9af3e33603bf389e5b337ee5bdbc9558b9">positive</a>);</div>
<div class="line"> <a class="code" href="xsample08_8cpp.html#a704b4ac4464e1c71312fb580b441a0be">add_object</a>(dm, 4, 70, <a class="code" href="xsample08_8cpp.html#a6aeede226b1f5324cd2f58cbc64c38c9a7b1174d620ccd8d2a049d8440aa1fc4d">negative</a>);</div>
<div class="line"> <a class="code" href="xsample08_8cpp.html#a704b4ac4464e1c71312fb580b441a0be">add_object</a>(dm, 15, 20, <a class="code" href="xsample08_8cpp.html#a6aeede226b1f5324cd2f58cbc64c38c9a7b1174d620ccd8d2a049d8440aa1fc4d">negative</a>);</div>
<div class="line"> <a class="code" href="xsample08_8cpp.html#a704b4ac4464e1c71312fb580b441a0be">add_object</a>(dm, 20, 30, <a class="code" href="xsample08_8cpp.html#a6aeede226b1f5324cd2f58cbc64c38c9af3e33603bf389e5b337ee5bdbc9558b9">positive</a>);</div>
<div class="line"> <a class="code" href="xsample08_8cpp.html#a704b4ac4464e1c71312fb580b441a0be">add_object</a>(dm, 16, 21, <a class="code" href="xsample08_8cpp.html#a6aeede226b1f5324cd2f58cbc64c38c9a5b9f6d065e6e98483b3d3ed01f4f6cbe">unknown</a>);</div>
<div class="line"> </div>
<div class="line"> dm.<a class="code" href="structdata__model.html#a0444be6631839b756ec5b9f16c5f0567">optimize</a>(); <span class="comment">// run compression and build access index</span></div>
<div class="line"> </div>
<div class="line"> <span class="comment">// View the model using toy ASCII art renderer</span></div>
<div class="line"> <span class="comment">//</span></div>
<div class="line"> <a class="code" href="xsample08_8cpp.html#af5053305a6d00802a606429f4cceaa9c">print_model</a>(dm);</div>
<div class="line"> </div>
<div class="line"> <span class="comment">// create a model splice for [5..10] range</span></div>
<div class="line"> <span class="comment">// plus drop strand property (renderer will assume unknown)</span></div>
<div class="line"> <span class="comment">//</span></div>
<div class="line"> {</div>
<div class="line"> <a class="code" href="structdata__model.html">data_model</a> dm_splice;</div>
<div class="line"> </div>
<div class="line"> <a class="code" href="xsample08_8cpp.html#a6dc270468776be32b200c6722489c91b">splice_model</a>(dm_splice, dm, 5, 10, <span class="keyword">false</span>);</div>
<div class="line"> dm_splice.<a class="code" href="structdata__model.html#a0444be6631839b756ec5b9f16c5f0567">optimize</a>();</div>
<div class="line"> </div>
<div class="line"> cout << endl;</div>
<div class="line"> <a class="code" href="xsample08_8cpp.html#af5053305a6d00802a606429f4cceaa9c">print_model</a>(dm_splice);</div>
<div class="line"> }</div>
<div class="line"> </div>
<div class="line"> <span class="comment">// create a model splice for [5..10] range</span></div>
<div class="line"> <span class="comment">// now WITH strand property</span></div>
<div class="line"> <span class="comment">//</span></div>
<div class="line"> {</div>
<div class="line"> <a class="code" href="structdata__model.html">data_model</a> dm_splice;</div>
<div class="line"> </div>
<div class="line"> <a class="code" href="xsample08_8cpp.html#a6dc270468776be32b200c6722489c91b">splice_model</a>(dm_splice, dm, 5, 10, <span class="keyword">true</span>);</div>
<div class="line"> dm_splice.<a class="code" href="structdata__model.html#a0444be6631839b756ec5b9f16c5f0567">optimize</a>();</div>
<div class="line"> </div>
<div class="line"> cout << endl;</div>
<div class="line"> <a class="code" href="xsample08_8cpp.html#af5053305a6d00802a606429f4cceaa9c">print_model</a>(dm_splice);</div>
<div class="line"> }</div>
<div class="line"> }</div>
<div class="line"> <span class="keywordflow">catch</span>(std::exception& ex)</div>
<div class="line"> {</div>
<div class="line"> std::cerr << ex.what() << std::endl;</div>
<div class="line"> <span class="keywordflow">return</span> 1;</div>
<div class="line"> }</div>
<div class="line"> </div>
<div class="line"> <span class="keywordflow">return</span> 0;</div>
<div class="line">}</div>
<div class="line"> </div>
</div><!-- fragment --> </div><!-- contents -->
<div class="ttc" id="aclassbm_1_1bvector_html_aafb2ecaa1a55856533e6b4afbf788eae"><div class="ttname"><a href="classbm_1_1bvector.html#aafb2ecaa1a55856533e6b4afbf788eae">bm::bvector::set_range</a></div><div class="ttdeci">bvector< Alloc > & set_range(size_type left, size_type right, bool value=true)</div><div class="ttdoc">Sets all bits in the specified closed interval [left,right] Interval must be inside the bvector's siz...</div><div class="ttdef"><b>Definition:</b> <a href="bm_8h_source.html#l02158">bm.h:2158</a></div></div>
<div class="ttc" id="aclassbm_1_1rsc__sparse__vector_html_a3fcda99085ab1d9f9cca1a6ce48f543e"><div class="ttname"><a href="classbm_1_1rsc__sparse__vector.html#a3fcda99085ab1d9f9cca1a6ce48f543e">bm::rsc_sparse_vector::set</a></div><div class="ttdeci">void set(size_type idx, value_type v)</div><div class="ttdoc">set specified element with bounds checking and automatic resize</div><div class="ttdef"><b>Definition:</b> <a href="bmsparsevec__compr_8h_source.html#l00847">bmsparsevec_compr.h:847</a></div></div>
<div class="ttc" id="astructdata__model_html_ad02501c19c47ee7f99a74a7cd8a6f2da"><div class="ttname"><a href="structdata__model.html#ad02501c19c47ee7f99a74a7cd8a6f2da">data_model::layout_v</a></div><div class="ttdeci">layout_vector_type layout_v</div><div class="ttdoc">layout vector</div><div class="ttdef"><b>Definition:</b> <a href="xsample08_8cpp_source.html#l00085">xsample08.cpp:85</a></div></div>
<div class="ttc" id="aclassbm_1_1sparse__vector_html"><div class="ttname"><a href="classbm_1_1sparse__vector.html">bm::sparse_vector</a></div><div class="ttdoc">sparse vector with runtime compression using bit transposition method</div><div class="ttdef"><b>Definition:</b> <a href="bmsparsevec_8h_source.html#l00081">bmsparsevec.h:81</a></div></div>
<div class="ttc" id="astructdata__model_html_a0444be6631839b756ec5b9f16c5f0567"><div class="ttname"><a href="structdata__model.html#a0444be6631839b756ec5b9f16c5f0567">data_model::optimize</a></div><div class="ttdeci">void optimize()</div><div class="ttdoc">Optimize memory layoput, build index for faster read access.</div><div class="ttdef"><b>Definition:</b> <a href="xsample08_8cpp_source.html#l00089">xsample08.cpp:89</a></div></div>
<div class="ttc" id="abm_8h_html_ad9736d9521d713fa5d48859aa720bfdd"><div class="ttname"><a href="bm_8h.html#ad9736d9521d713fa5d48859aa720bfdd">BM_DECLARE_TEMP_BLOCK</a></div><div class="ttdeci">#define BM_DECLARE_TEMP_BLOCK(x)</div><div class="ttdef"><b>Definition:</b> <a href="bm_8h_source.html#l00047">bm.h:47</a></div></div>
<div class="ttc" id="astructdata__model_html_a2b5714a796e1485b7ea503d6c9f8ba02"><div class="ttname"><a href="structdata__model.html#a2b5714a796e1485b7ea503d6c9f8ba02">data_model::add_strand</a></div><div class="ttdeci">void add_strand(size_t plane, rsc_vector_u8 *strand)</div><div class="ttdef"><b>Definition:</b> <a href="xsample08_8cpp_source.html#l00124">xsample08.cpp:124</a></div></div>
<div class="ttc" id="axsample08_8cpp_html_a6dc270468776be32b200c6722489c91b"><div class="ttname"><a href="xsample08_8cpp.html#a6dc270468776be32b200c6722489c91b">splice_model</a></div><div class="ttdeci">void splice_model(data_model &dm_target, const data_model &dm, bm::bvector<>::size_type start, bm::bvector<>::size_type end, bool copy_strands)</div><div class="ttdoc">Data model splicer.</div><div class="ttdef"><b>Definition:</b> <a href="xsample08_8cpp_source.html#l00208">xsample08.cpp:208</a></div></div>
<div class="ttc" id="agroup__bvintervals_html_gaa184975ff6e9b314ab559f132e730880"><div class="ttname"><a href="group__bvintervals.html#gaa184975ff6e9b314ab559f132e730880">bm::find_interval_start</a></div><div class="ttdeci">bool find_interval_start(const BV &bv, typename BV::size_type from, typename BV::size_type &pos) BMNOEXCEPT</div><div class="ttdoc">Reverse find index of first 1 bit gap (01110) starting from position Reverse scan for the first 1 in ...</div><div class="ttdef"><b>Definition:</b> <a href="bmintervals_8h_source.html#l00315">bmintervals.h:315</a></div></div>
<div class="ttc" id="axsample08_8cpp_html_a4818975b7767c5d423cbc0f181261cf4"><div class="ttname"><a href="xsample08_8cpp.html#a4818975b7767c5d423cbc0f181261cf4">interval_enumerator_type</a></div><div class="ttdeci">bm::interval_enumerator< bm::bvector<> > interval_enumerator_type</div><div class="ttdef"><b>Definition:</b> <a href="xsample08_8cpp_source.html#l00063">xsample08.cpp:63</a></div></div>
<div class="ttc" id="axsample08_8cpp_html_a624e05d875c1dd02606ea289d96d9c62"><div class="ttname"><a href="xsample08_8cpp.html#a624e05d875c1dd02606ea289d96d9c62">rsc_vector_u8</a></div><div class="ttdeci">bm::rsc_sparse_vector< unsigned char, sparse_vector_u8 > rsc_vector_u8</div><div class="ttdef"><b>Definition:</b> <a href="xsample08_8cpp_source.html#l00067">xsample08.cpp:67</a></div></div>
<div class="ttc" id="axsample08_8cpp_html_a6aeede226b1f5324cd2f58cbc64c38c9"><div class="ttname"><a href="xsample08_8cpp.html#a6aeede226b1f5324cd2f58cbc64c38c9">Strand</a></div><div class="ttdeci">Strand</div><div class="ttdef"><b>Definition:</b> <a href="xsample08_8cpp_source.html#l00320">xsample08.cpp:320</a></div></div>
<div class="ttc" id="astructdata__model_html"><div class="ttname"><a href="structdata__model.html">data_model</a></div><div class="ttdoc">Data frame object, sued to buid succinct data model.</div><div class="ttdef"><b>Definition:</b> <a href="xsample08_8cpp_source.html#l00076">xsample08.cpp:76</a></div></div>
<div class="ttc" id="abmsparsevec__compr_8h_html"><div class="ttname"><a href="bmsparsevec__compr_8h.html">bmsparsevec_compr.h</a></div><div class="ttdoc">Compressed sparse container rsc_sparse_vector<> for integer types.</div></div>
<div class="ttc" id="aclassbm_1_1bvector_html"><div class="ttname"><a href="classbm_1_1bvector.html">bm::bvector<></a></div></div>
<div class="ttc" id="axsample08_8cpp_html_a570a10a183b6108efc4df372793d0563"><div class="ttname"><a href="xsample08_8cpp.html#a570a10a183b6108efc4df372793d0563">starnds_vector_type</a></div><div class="ttdeci">std::vector< std::unique_ptr< rsc_vector_u8 > > starnds_vector_type</div><div class="ttdef"><b>Definition:</b> <a href="xsample08_8cpp_source.html#l00068">xsample08.cpp:68</a></div></div>
<div class="ttc" id="astructdata__model_html_ae98a6571059d2235083b08aca3957cfc"><div class="ttname"><a href="structdata__model.html#ae98a6571059d2235083b08aca3957cfc">data_model::strand_v</a></div><div class="ttdeci">starnds_vector_type strand_v</div><div class="ttdoc">strand planes vector</div><div class="ttdef"><b>Definition:</b> <a href="xsample08_8cpp_source.html#l00086">xsample08.cpp:86</a></div></div>
<div class="ttc" id="axsample08_8cpp_html_a6aeede226b1f5324cd2f58cbc64c38c9a7b1174d620ccd8d2a049d8440aa1fc4d"><div class="ttname"><a href="xsample08_8cpp.html#a6aeede226b1f5324cd2f58cbc64c38c9a7b1174d620ccd8d2a049d8440aa1fc4d">negative</a></div><div class="ttdeci">@ negative</div><div class="ttdef"><b>Definition:</b> <a href="xsample08_8cpp_source.html#l00320">xsample08.cpp:320</a></div></div>
<div class="ttc" id="aclassbm_1_1rsc__sparse__vector_html_aa8e0eeff8947aac3899ee79d5c040ca9"><div class="ttname"><a href="classbm_1_1rsc__sparse__vector.html#aa8e0eeff8947aac3899ee79d5c040ca9">bm::rsc_sparse_vector::is_null</a></div><div class="ttdeci">bool is_null(size_type idx) const BMNOEXCEPT</div><div class="ttdoc">test if specified element is NULL</div><div class="ttdef"><b>Definition:</b> <a href="bmsparsevec__compr_8h_source.html#l01071">bmsparsevec_compr.h:1071</a></div></div>
<div class="ttc" id="axsample08_8cpp_html_a704b4ac4464e1c71312fb580b441a0be"><div class="ttname"><a href="xsample08_8cpp.html#a704b4ac4464e1c71312fb580b441a0be">add_object</a></div><div class="ttdeci">void add_object(data_model &dm, unsigned start, unsigned end, unsigned char strand)</div><div class="ttdoc">Register new object in the data model: [start..end] + strand.</div><div class="ttdef"><b>Definition:</b> <a href="xsample08_8cpp_source.html#l00166">xsample08.cpp:166</a></div></div>
<div class="ttc" id="axsample08_8cpp_html_af276e5a029922cc9fe0803b63a8eb363"><div class="ttname"><a href="xsample08_8cpp.html#af276e5a029922cc9fe0803b63a8eb363">layout_vector_type</a></div><div class="ttdeci">std::vector< std::unique_ptr< bm::bvector<> > > layout_vector_type</div><div class="ttdef"><b>Definition:</b> <a href="xsample08_8cpp_source.html#l00064">xsample08.cpp:64</a></div></div>
<div class="ttc" id="axsample08_8cpp_html_a94126954222ad24c55587827067e134d"><div class="ttname"><a href="xsample08_8cpp.html#a94126954222ad24c55587827067e134d">set_feature_strand</a></div><div class="ttdeci">void set_feature_strand(data_model &dm, size_t plane, bm::bvector<>::size_type pos, unsigned char strand)</div><div class="ttdef"><b>Definition:</b> <a href="xsample08_8cpp_source.html#l00142">xsample08.cpp:142</a></div></div>
<div class="ttc" id="agroup__bvector_html_ggad0b87b3b7292383a864d27feaf1c9effa7fe09d1d7c62a813db922c396c0cbc9c"><div class="ttname"><a href="group__bvector.html#ggad0b87b3b7292383a864d27feaf1c9effa7fe09d1d7c62a813db922c396c0cbc9c">bm::BM_GAP</a></div><div class="ttdeci">@ BM_GAP</div><div class="ttdoc">GAP compression is ON.</div><div class="ttdef"><b>Definition:</b> <a href="bmconst_8h_source.html#l00144">bmconst.h:144</a></div></div>
<div class="ttc" id="aclassbm_1_1bvector_html_a530f12c9a00799ecbe9abd276a7ae619"><div class="ttname"><a href="classbm_1_1bvector.html#a530f12c9a00799ecbe9abd276a7ae619">bm::bvector::any_range</a></div><div class="ttdeci">bool any_range(size_type left, size_type right) const BMNOEXCEPT</div><div class="ttdoc">Returns true if any bits in the range are 1s (non-empty interval) Function uses closed interval [left...</div><div class="ttdef"><b>Definition:</b> <a href="bm_8h_source.html#l02865">bm.h:2865</a></div></div>
<div class="ttc" id="astructdata__model_html_a5c626772440999a94b6f3ce851bc916f"><div class="ttname"><a href="structdata__model.html#a5c626772440999a94b6f3ce851bc916f">data_model::add_layout</a></div><div class="ttdeci">void add_layout(size_t plane, bm::bvector<> *bv)</div><div class="ttdef"><b>Definition:</b> <a href="xsample08_8cpp_source.html#l00109">xsample08.cpp:109</a></div></div>
<div class="ttc" id="abmintervals_8h_html"><div class="ttname"><a href="bmintervals_8h.html">bmintervals.h</a></div><div class="ttdoc">Algorithms for bit ranges and intervals.</div></div>
<div class="ttc" id="axsample08_8cpp_html_a21ab0bc26ed51234f40ec4959e4e1868"><div class="ttname"><a href="xsample08_8cpp.html#a21ab0bc26ed51234f40ec4959e4e1868">sparse_vector_u8</a></div><div class="ttdeci">bm::sparse_vector< unsigned char, bm::bvector<> > sparse_vector_u8</div><div class="ttdef"><b>Definition:</b> <a href="xsample08_8cpp_source.html#l00066">xsample08.cpp:66</a></div></div>
<div class="ttc" id="aclassbm_1_1rsc__sparse__vector_html"><div class="ttname"><a href="classbm_1_1rsc__sparse__vector.html">bm::rsc_sparse_vector</a></div><div class="ttdoc">Rank-Select compressed sparse vector.</div><div class="ttdef"><b>Definition:</b> <a href="bmsparsevec__compr_8h_source.html#l00058">bmsparsevec_compr.h:58</a></div></div>
<div class="ttc" id="axsample08_8cpp_html_a840291bc02cba5474a4cb46a9b9566fe"><div class="ttname"><a href="xsample08_8cpp.html#a840291bc02cba5474a4cb46a9b9566fe">main</a></div><div class="ttdeci">int main(void)</div><div class="ttdef"><b>Definition:</b> <a href="xsample08_8cpp_source.html#l00324">xsample08.cpp:324</a></div></div>
<div class="ttc" id="axsample08_8cpp_html_af5053305a6d00802a606429f4cceaa9c"><div class="ttname"><a href="xsample08_8cpp.html#af5053305a6d00802a606429f4cceaa9c">print_model</a></div><div class="ttdeci">void print_model(const data_model &dm)</div><div class="ttdoc">This is ASCII art "renderer" for the data model.</div><div class="ttdef"><b>Definition:</b> <a href="xsample08_8cpp_source.html#l00265">xsample08.cpp:265</a></div></div>
<div class="ttc" id="aclassbm_1_1bvector_html_a937cd13482984f234a5d94cc638c22b5"><div class="ttname"><a href="classbm_1_1bvector.html#a937cd13482984f234a5d94cc638c22b5">bm::bvector::end</a></div><div class="ttdeci">enumerator end() const</div><div class="ttdoc">Returns enumerator pointing on the next bit after the last.</div><div class="ttdef"><b>Definition:</b> <a href="bm_8h_source.html#l01776">bm.h:1776</a></div></div>
<div class="ttc" id="aclassbm_1_1interval__enumerator_html"><div class="ttname"><a href="classbm_1_1interval__enumerator.html">bm::interval_enumerator</a></div><div class="ttdoc">forward iterator class to traverse bit-vector as ranges</div><div class="ttdef"><b>Definition:</b> <a href="bmintervals_8h_source.html#l00052">bmintervals.h:52</a></div></div>
<div class="ttc" id="axsample08_8cpp_html_a6aeede226b1f5324cd2f58cbc64c38c9af3e33603bf389e5b337ee5bdbc9558b9"><div class="ttname"><a href="xsample08_8cpp.html#a6aeede226b1f5324cd2f58cbc64c38c9af3e33603bf389e5b337ee5bdbc9558b9">positive</a></div><div class="ttdeci">@ positive</div><div class="ttdef"><b>Definition:</b> <a href="xsample08_8cpp_source.html#l00320">xsample08.cpp:320</a></div></div>
<div class="ttc" id="axsample08_8cpp_html_a6aeede226b1f5324cd2f58cbc64c38c9a5b9f6d065e6e98483b3d3ed01f4f6cbe"><div class="ttname"><a href="xsample08_8cpp.html#a6aeede226b1f5324cd2f58cbc64c38c9a5b9f6d065e6e98483b3d3ed01f4f6cbe">unknown</a></div><div class="ttdeci">@ unknown</div><div class="ttdef"><b>Definition:</b> <a href="xsample08_8cpp_source.html#l00320">xsample08.cpp:320</a></div></div>
<div class="ttc" id="aclassbm_1_1bvector_html_a405dd9ed048c935c84a5086ec8ba3649"><div class="ttname"><a href="classbm_1_1bvector.html#a405dd9ed048c935c84a5086ec8ba3649">bm::bvector::size_type</a></div><div class="ttdeci">bm::id_t size_type</div><div class="ttdef"><b>Definition:</b> <a href="bm_8h_source.html#l00117">bm.h:117</a></div></div>
<div class="ttc" id="abm_8h_html"><div class="ttname"><a href="bm_8h.html">bm.h</a></div><div class="ttdoc">Compressed bit-vector bvector<> container, set algebraic methods, traversal iterators.</div></div>
<div class="ttc" id="agroup__bvintervals_html_ga41642899622fcb337ef94b6861f40f92"><div class="ttname"><a href="group__bvintervals.html#ga41642899622fcb337ef94b6861f40f92">bm::find_interval_end</a></div><div class="ttdeci">bool find_interval_end(const BV &bv, typename BV::size_type from, typename BV::size_type &pos) BMNOEXCEPT</div><div class="ttdoc">Reverse find index of first 1 bit gap (01110) starting from position Reverse scan for the first 1 in ...</div><div class="ttdef"><b>Definition:</b> <a href="bmintervals_8h_source.html#l00438">bmintervals.h:438</a></div></div>
<div class="ttc" id="aclassbm_1_1rsc__sparse__vector_html_a90d532ba181599d75564153bc71a84fa"><div class="ttname"><a href="classbm_1_1rsc__sparse__vector.html#a90d532ba181599d75564153bc71a84fa">bm::rsc_sparse_vector::get</a></div><div class="ttdeci">value_type get(size_type idx) const BMNOEXCEPT</div><div class="ttdoc">get specified element without bounds checking</div><div class="ttdef"><b>Definition:</b> <a href="bmsparsevec__compr_8h_source.html#l01058">bmsparsevec_compr.h:1058</a></div></div>
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