svf-tools 1.0.595 → 1.0.596

package/SVF-doxygen/html/html/fastcluster__R__dm_8cpp_8inc_source.html

@@ -66,7 +66,8 @@ $(function() {
 <div class="title">fastcluster_R_dm.cpp.inc</div>  </div>
 </div><!--header-->
 <div class="contents">
-<a href="fastcluster__R__dm_8cpp_8inc.html">Go to the documentation of this file.</a><div class="fragment"><div class="line"><a name="l00001"></a><span class="lineno">    1</span>&#160;<span class="comment">//</span></div><div class="line"><a name="l00002"></a><span class="lineno">    2</span>&#160;<span class="comment">// Excerpt from fastcluster_R.cpp</span></div><div class="line"><a name="l00003"></a><span class="lineno">    3</span>&#160;<span class="comment">//</span></div><div class="line"><a name="l00004"></a><span class="lineno">    4</span>&#160;<span class="comment">// Copyright: Daniel Müllner, 2011 &lt;http://danifold.net&gt;</span></div><div class="line"><a name="l00005"></a><span class="lineno">    5</span>&#160;<span class="comment">//</span></div><div class="line"><a name="l00006"></a><span class="lineno">    6</span>&#160;</div><div class="line"><a name="l00007"></a><span class="lineno">    7</span>&#160;<span class="keyword">struct </span>pos_node {</div><div class="line"><a name="l00008"></a><span class="lineno">    8</span>&#160;  t_index pos;</div><div class="line"><a name="l00009"></a><span class="lineno">    9</span>&#160;  <span class="keywordtype">int</span> node;</div><div class="line"><a name="l00010"></a><span class="lineno">   10</span>&#160;};</div><div class="line"><a name="l00011"></a><span class="lineno">   11</span>&#160;</div><div class="line"><a name="l00012"></a><span class="lineno">   12</span>&#160;<span class="keywordtype">void</span> order_nodes(<span class="keyword">const</span> <span class="keywordtype">int</span> N, <span class="keyword">const</span> <span class="keywordtype">int</span> * <span class="keyword">const</span> merge, <span class="keyword">const</span> t_index * <span class="keyword">const</span> node_size, <span class="keywordtype">int</span> * <span class="keyword">const</span> order) {</div><div class="line"><a name="l00013"></a><span class="lineno">   13</span>&#160;  <span class="comment">/* Parameters:</span></div><div class="line"><a name="l00014"></a><span class="lineno">   14</span>&#160;<span class="comment">     N         : number of data points</span></div><div class="line"><a name="l00015"></a><span class="lineno">   15</span>&#160;<span class="comment">     merge     : (N-1)×2 array which specifies the node indices which are</span></div><div class="line"><a name="l00016"></a><span class="lineno">   16</span>&#160;<span class="comment">                 merged in each step of the clustering procedure.</span></div><div class="line"><a name="l00017"></a><span class="lineno">   17</span>&#160;<span class="comment">                 Negative entries -1...-N point to singleton nodes, while</span></div><div class="line"><a name="l00018"></a><span class="lineno">   18</span>&#160;<span class="comment">                 positive entries 1...(N-1) point to nodes which are themselves</span></div><div class="line"><a name="l00019"></a><span class="lineno">   19</span>&#160;<span class="comment">                 parents of other nodes.</span></div><div class="line"><a name="l00020"></a><span class="lineno">   20</span>&#160;<span class="comment">     node_size : array of node sizes - makes it easier</span></div><div class="line"><a name="l00021"></a><span class="lineno">   21</span>&#160;<span class="comment">     order     : output array of size N</span></div><div class="line"><a name="l00022"></a><span class="lineno">   22</span>&#160;<span class="comment"></span></div><div class="line"><a name="l00023"></a><span class="lineno">   23</span>&#160;<span class="comment">     Runtime: Θ(N)</span></div><div class="line"><a name="l00024"></a><span class="lineno">   24</span>&#160;<span class="comment">  */</span></div><div class="line"><a name="l00025"></a><span class="lineno">   25</span>&#160;  auto_array_ptr&lt;pos_node&gt; queue(N/2);</div><div class="line"><a name="l00026"></a><span class="lineno">   26</span>&#160;</div><div class="line"><a name="l00027"></a><span class="lineno">   27</span>&#160;  <span class="keywordtype">int</span> parent;</div><div class="line"><a name="l00028"></a><span class="lineno">   28</span>&#160;  <span class="keywordtype">int</span> <a class="code" href="cJSON_8cpp.html#ad00efb41ca386db28bacc7aefe79535c">child</a>;</div><div class="line"><a name="l00029"></a><span class="lineno">   29</span>&#160;  t_index pos = 0;</div><div class="line"><a name="l00030"></a><span class="lineno">   30</span>&#160;</div><div class="line"><a name="l00031"></a><span class="lineno">   31</span>&#160;  queue[0].pos = 0;</div><div class="line"><a name="l00032"></a><span class="lineno">   32</span>&#160;  queue[0].node = N-2;</div><div class="line"><a name="l00033"></a><span class="lineno">   33</span>&#160;  t_index idx = 1;</div><div class="line"><a name="l00034"></a><span class="lineno">   34</span>&#160;</div><div class="line"><a name="l00035"></a><span class="lineno">   35</span>&#160;  <span class="keywordflow">do</span> {</div><div class="line"><a name="l00036"></a><span class="lineno">   36</span>&#160;    --idx;</div><div class="line"><a name="l00037"></a><span class="lineno">   37</span>&#160;    pos = queue[idx].pos;</div><div class="line"><a name="l00038"></a><span class="lineno">   38</span>&#160;    parent = queue[idx].node;</div><div class="line"><a name="l00039"></a><span class="lineno">   39</span>&#160;</div><div class="line"><a name="l00040"></a><span class="lineno">   40</span>&#160;    <span class="comment">// First child</span></div><div class="line"><a name="l00041"></a><span class="lineno">   41</span>&#160;    child = merge[parent];</div><div class="line"><a name="l00042"></a><span class="lineno">   42</span>&#160;    <span class="keywordflow">if</span> (child&lt;0) { <span class="comment">// singleton node, write this into the &#39;order&#39; array.</span></div><div class="line"><a name="l00043"></a><span class="lineno">   43</span>&#160;      order[pos] = -<a class="code" href="cJSON_8cpp.html#ad00efb41ca386db28bacc7aefe79535c">child</a>;</div><div class="line"><a name="l00044"></a><span class="lineno">   44</span>&#160;      ++pos;</div><div class="line"><a name="l00045"></a><span class="lineno">   45</span>&#160;    }</div><div class="line"><a name="l00046"></a><span class="lineno">   46</span>&#160;    <span class="keywordflow">else</span> { <span class="comment">/* compound node: put it on top of the queue and decompose it</span></div><div class="line"><a name="l00047"></a><span class="lineno">   47</span>&#160;<span class="comment">              in a later iteration. */</span></div><div class="line"><a name="l00048"></a><span class="lineno">   48</span>&#160;      queue[idx].pos = pos;</div><div class="line"><a name="l00049"></a><span class="lineno">   49</span>&#160;      queue[idx].node = child-1; <span class="comment">// convert index-1 based to index-0 based</span></div><div class="line"><a name="l00050"></a><span class="lineno">   50</span>&#160;      ++idx;</div><div class="line"><a name="l00051"></a><span class="lineno">   51</span>&#160;      pos += node_size[child-1];</div><div class="line"><a name="l00052"></a><span class="lineno">   52</span>&#160;    }</div><div class="line"><a name="l00053"></a><span class="lineno">   53</span>&#160;    <span class="comment">// Second child</span></div><div class="line"><a name="l00054"></a><span class="lineno">   54</span>&#160;    child = merge[parent+N-1];</div><div class="line"><a name="l00055"></a><span class="lineno">   55</span>&#160;    <span class="keywordflow">if</span> (child&lt;0) {</div><div class="line"><a name="l00056"></a><span class="lineno">   56</span>&#160;      order[pos] = -<a class="code" href="cJSON_8cpp.html#ad00efb41ca386db28bacc7aefe79535c">child</a>;</div><div class="line"><a name="l00057"></a><span class="lineno">   57</span>&#160;    }</div><div class="line"><a name="l00058"></a><span class="lineno">   58</span>&#160;    <span class="keywordflow">else</span> {</div><div class="line"><a name="l00059"></a><span class="lineno">   59</span>&#160;      queue[idx].pos = pos;</div><div class="line"><a name="l00060"></a><span class="lineno">   60</span>&#160;      queue[idx].node = child-1;</div><div class="line"><a name="l00061"></a><span class="lineno">   61</span>&#160;      ++idx;</div><div class="line"><a name="l00062"></a><span class="lineno">   62</span>&#160;    }</div><div class="line"><a name="l00063"></a><span class="lineno">   63</span>&#160;  } <span class="keywordflow">while</span> (idx&gt;0);</div><div class="line"><a name="l00064"></a><span class="lineno">   64</span>&#160;}</div><div class="line"><a name="l00065"></a><span class="lineno">   65</span>&#160;</div><div class="line"><a name="l00066"></a><span class="lineno">   66</span>&#160;<span class="preprocessor">#define size_(r_) ( ((r_&lt;N) ? 1 : node_size[r_-N]) )</span></div><div class="line"><a name="l00067"></a><span class="lineno">   67</span>&#160;</div><div class="line"><a name="l00068"></a><span class="lineno">   68</span>&#160;<span class="keyword">template</span> &lt;const <span class="keywordtype">bool</span> sorted&gt;</div><div class="line"><a name="l00069"></a><span class="lineno">   69</span>&#160;<span class="keywordtype">void</span> generate_R_dendrogram(<span class="keywordtype">int</span> * <span class="keyword">const</span> merge, <span class="keywordtype">double</span> * <span class="keyword">const</span> height, <span class="keywordtype">int</span> * <span class="keyword">const</span> order, cluster_result &amp; Z2, <span class="keyword">const</span> <span class="keywordtype">int</span> N) {</div><div class="line"><a name="l00070"></a><span class="lineno">   70</span>&#160;  <span class="comment">// The array &quot;nodes&quot; is a union-find data structure for the cluster</span></div><div class="line"><a name="l00071"></a><span class="lineno">   71</span>&#160;  <span class="comment">// identites (only needed for unsorted cluster_result input).</span></div><div class="line"><a name="l00072"></a><span class="lineno">   72</span>&#160;  union_find nodes(sorted ? 0 : N);</div><div class="line"><a name="l00073"></a><span class="lineno">   73</span>&#160;  <span class="keywordflow">if</span> (!sorted) {</div><div class="line"><a name="l00074"></a><span class="lineno">   74</span>&#160;    std::stable_sort(Z2[0], Z2[N-1]);</div><div class="line"><a name="l00075"></a><span class="lineno">   75</span>&#160;  }</div><div class="line"><a name="l00076"></a><span class="lineno">   76</span>&#160;</div><div class="line"><a name="l00077"></a><span class="lineno">   77</span>&#160;  t_index node1, node2;</div><div class="line"><a name="l00078"></a><span class="lineno">   78</span>&#160;  auto_array_ptr&lt;t_index&gt; node_size(N-1);</div><div class="line"><a name="l00079"></a><span class="lineno">   79</span>&#160;</div><div class="line"><a name="l00080"></a><span class="lineno">   80</span>&#160;  <span class="keywordflow">for</span> (t_index i=0; i&lt;N-1; ++i) {</div><div class="line"><a name="l00081"></a><span class="lineno">   81</span>&#160;    <span class="comment">// Get two data points whose clusters are merged in step i.</span></div><div class="line"><a name="l00082"></a><span class="lineno">   82</span>&#160;    <span class="comment">// Find the cluster identifiers for these points.</span></div><div class="line"><a name="l00083"></a><span class="lineno">   83</span>&#160;    <span class="keywordflow">if</span> (sorted) {</div><div class="line"><a name="l00084"></a><span class="lineno">   84</span>&#160;      node1 = Z2[i]-&gt;node1;</div><div class="line"><a name="l00085"></a><span class="lineno">   85</span>&#160;      node2 = Z2[i]-&gt;node2;</div><div class="line"><a name="l00086"></a><span class="lineno">   86</span>&#160;    }</div><div class="line"><a name="l00087"></a><span class="lineno">   87</span>&#160;    <span class="keywordflow">else</span> {</div><div class="line"><a name="l00088"></a><span class="lineno">   88</span>&#160;      node1 = nodes.Find(Z2[i]-&gt;node1);</div><div class="line"><a name="l00089"></a><span class="lineno">   89</span>&#160;      node2 = nodes.Find(Z2[i]-&gt;node2);</div><div class="line"><a name="l00090"></a><span class="lineno">   90</span>&#160;      <span class="comment">// Merge the nodes in the union-find data structure by making them</span></div><div class="line"><a name="l00091"></a><span class="lineno">   91</span>&#160;      <span class="comment">// children of a new node.</span></div><div class="line"><a name="l00092"></a><span class="lineno">   92</span>&#160;      nodes.Union(node1, node2);</div><div class="line"><a name="l00093"></a><span class="lineno">   93</span>&#160;    }</div><div class="line"><a name="l00094"></a><span class="lineno">   94</span>&#160;    <span class="comment">// Sort the nodes in the output array.</span></div><div class="line"><a name="l00095"></a><span class="lineno">   95</span>&#160;    <span class="keywordflow">if</span> (node1&gt;node2) {</div><div class="line"><a name="l00096"></a><span class="lineno">   96</span>&#160;      t_index tmp = node1;</div><div class="line"><a name="l00097"></a><span class="lineno">   97</span>&#160;      node1 = node2;</div><div class="line"><a name="l00098"></a><span class="lineno">   98</span>&#160;      node2 = tmp;</div><div class="line"><a name="l00099"></a><span class="lineno">   99</span>&#160;    }</div><div class="line"><a name="l00100"></a><span class="lineno">  100</span>&#160;    <span class="comment">/* Conversion between labeling conventions.</span></div><div class="line"><a name="l00101"></a><span class="lineno">  101</span>&#160;<span class="comment">       Input:  singleton nodes 0,...,N-1</span></div><div class="line"><a name="l00102"></a><span class="lineno">  102</span>&#160;<span class="comment">               compound nodes  N,...,2N-2</span></div><div class="line"><a name="l00103"></a><span class="lineno">  103</span>&#160;<span class="comment">       Output: singleton nodes -1,...,-N</span></div><div class="line"><a name="l00104"></a><span class="lineno">  104</span>&#160;<span class="comment">               compound nodes  1,...,N</span></div><div class="line"><a name="l00105"></a><span class="lineno">  105</span>&#160;<span class="comment">    */</span></div><div class="line"><a name="l00106"></a><span class="lineno">  106</span>&#160;    merge[i]     = (node1&lt;N) ? -static_cast&lt;int&gt;(node1)-1</div><div class="line"><a name="l00107"></a><span class="lineno">  107</span>&#160;                              : <span class="keyword">static_cast&lt;</span><span class="keywordtype">int</span><span class="keyword">&gt;</span>(node1)-N+1;</div><div class="line"><a name="l00108"></a><span class="lineno">  108</span>&#160;    merge[i+N-1] = (node2&lt;N) ? -static_cast&lt;int&gt;(node2)-1</div><div class="line"><a name="l00109"></a><span class="lineno">  109</span>&#160;                              : <span class="keyword">static_cast&lt;</span><span class="keywordtype">int</span><span class="keyword">&gt;</span>(node2)-N+1;</div><div class="line"><a name="l00110"></a><span class="lineno">  110</span>&#160;    height[i] = Z2[i]-&gt;dist;</div><div class="line"><a name="l00111"></a><span class="lineno">  111</span>&#160;    node_size[i] = size_(node1) + size_(node2);</div><div class="line"><a name="l00112"></a><span class="lineno">  112</span>&#160;  }</div><div class="line"><a name="l00113"></a><span class="lineno">  113</span>&#160;</div><div class="line"><a name="l00114"></a><span class="lineno">  114</span>&#160;  order_nodes(N, merge, node_size, order);</div><div class="line"><a name="l00115"></a><span class="lineno">  115</span>&#160;}</div><div class="ttc" id="cJSON_8cpp_html_ad00efb41ca386db28bacc7aefe79535c"><div class="ttname"><a href="cJSON_8cpp.html#ad00efb41ca386db28bacc7aefe79535c">child</a></div><div class="ttdeci">cJSON * child</div><div class="ttdef"><b>Definition:</b> <a href="cJSON_8cpp_source.html#l02723">cJSON.cpp:2723</a></div></div>
+<a href="fastcluster__R__dm_8cpp_8inc.html">Go to the documentation of this file.</a><div class="fragment"><div class="line"><a name="l00001"></a><span class="lineno">    1</span>&#160;<span class="comment">//</span></div><div class="line"><a name="l00002"></a><span class="lineno">    2</span>&#160;<span class="comment">// Excerpt from fastcluster_R.cpp</span></div><div class="line"><a name="l00003"></a><span class="lineno">    3</span>&#160;<span class="comment">//</span></div><div class="line"><a name="l00004"></a><span class="lineno">    4</span>&#160;<span class="comment">// Copyright: Daniel Müllner, 2011 &lt;http://danifold.net&gt;</span></div><div class="line"><a name="l00005"></a><span class="lineno">    5</span>&#160;<span class="comment">//</span></div><div class="line"><a name="l00006"></a><span class="lineno">    6</span>&#160;</div><div class="line"><a name="l00007"></a><span class="lineno">    7</span>&#160;<span class="keyword">struct </span>pos_node {</div><div class="line"><a name="l00008"></a><span class="lineno">    8</span>&#160;  t_index pos;</div><div class="line"><a name="l00009"></a><span class="lineno">    9</span>&#160;  <span class="keywordtype">int</span> node;</div><div class="line"><a name="l00010"></a><span class="lineno">   10</span>&#160;};</div><div class="line"><a name="l00011"></a><span class="lineno">   11</span>&#160;</div><div class="line"><a name="l00012"></a><span class="lineno">   12</span>&#160;<span class="keywordtype">void</span> order_nodes(<span class="keyword">const</span> <span class="keywordtype">int</span> N, <span class="keyword">const</span> <span class="keywordtype">int</span> * <span class="keyword">const</span> merge, <span class="keyword">const</span> t_index * <span class="keyword">const</span> node_size, <span class="keywordtype">int</span> * <span class="keyword">const</span> order) {</div><div class="line"><a name="l00013"></a><span class="lineno">   13</span>&#160;  <span class="comment">/* Parameters:</span></div><div class="line"><a name="l00014"></a><span class="lineno">   14</span>&#160;<span class="comment">     N         : number of data points</span></div><div class="line"><a name="l00015"></a><span class="lineno">   15</span>&#160;<span class="comment">     merge     : (N-1)×2 array which specifies the node indices which are</span></div><div class="line"><a name="l00016"></a><span class="lineno">   16</span>&#160;<span class="comment">                 merged in each step of the clustering procedure.</span></div><div class="line"><a name="l00017"></a><span class="lineno">   17</span>&#160;<span class="comment">                 Negative entries -1...-N point to singleton nodes, while</span></div><div class="line"><a name="l00018"></a><span class="lineno">   18</span>&#160;<span class="comment">                 positive entries 1...(N-1) point to nodes which are themselves</span></div><div class="line"><a name="l00019"></a><span class="lineno">   19</span>&#160;<span class="comment">                 parents of other nodes.</span></div><div class="line"><a name="l00020"></a><span class="lineno">   20</span>&#160;<span class="comment">     node_size : array of node sizes - makes it easier</span></div><div class="line"><a name="l00021"></a><span class="lineno">   21</span>&#160;<span class="comment">     order     : output array of size N</span></div><div class="line"><a name="l00022"></a><span class="lineno">   22</span>&#160;<span class="comment"></span></div><div class="line"><a name="l00023"></a><span class="lineno">   23</span>&#160;<span class="comment">     Runtime: Θ(N)</span></div><div class="line"><a name="l00024"></a><span class="lineno">   24</span>&#160;<span class="comment">  */</span></div><div class="line"><a name="l00025"></a><span class="lineno">   25</span>&#160;  auto_array_ptr&lt;pos_node&gt; queue(N/2);</div><div class="line"><a name="l00026"></a><span class="lineno">   26</span>&#160;</div><div class="line"><a name="l00027"></a><span class="lineno">   27</span>&#160;  <span class="keywordtype">int</span> parent;</div><div class="line"><a name="l00028"></a><span class="lineno">   28</span>&#160;  <span class="keywordtype">int</span> <a class="code" href="cJSON_8cpp.html#ad00efb41ca386db28bacc7aefe79535c">child</a>;</div><div class="line"><a name="l00029"></a><span class="lineno">   29</span>&#160;  t_index pos = 0;</div><div class="line"><a name="l00030"></a><span class="lineno">   30</span>&#160;</div><div class="line"><a name="l00031"></a><span class="lineno">   31</span>&#160;  queue[0].pos = 0;</div><div class="line"><a name="l00032"></a><span class="lineno">   32</span>&#160;  queue[0].node = N-2;</div><div class="line"><a name="l00033"></a><span class="lineno">   33</span>&#160;  t_index idx = 1;</div><div class="line"><a name="l00034"></a><span class="lineno">   34</span>&#160;</div><div class="line"><a name="l00035"></a><span class="lineno">   35</span>&#160;  <span class="keywordflow">do</span> {</div><div class="line"><a name="l00036"></a><span class="lineno">   36</span>&#160;    --idx;</div><div class="line"><a name="l00037"></a><span class="lineno">   37</span>&#160;    pos = queue[idx].pos;</div><div class="line"><a name="l00038"></a><span class="lineno">   38</span>&#160;    parent = queue[idx].node;</div><div class="line"><a name="l00039"></a><span class="lineno">   39</span>&#160;</div><div class="line"><a name="l00040"></a><span class="lineno">   40</span>&#160;    <span class="comment">// First child</span></div><div class="line"><a name="l00041"></a><span class="lineno">   41</span>&#160;    child = merge[parent];</div><div class="line"><a name="l00042"></a><span class="lineno">   42</span>&#160;    <span class="keywordflow">if</span> (child&lt;0) { <span class="comment">// singleton node, write this into the &#39;order&#39; array.</span></div><div class="line"><a name="l00043"></a><span class="lineno">   43</span>&#160;      order[pos] = -<a class="code" href="cJSON_8cpp.html#ad00efb41ca386db28bacc7aefe79535c">child</a>;</div><div class="line"><a name="l00044"></a><span class="lineno">   44</span>&#160;      ++pos;</div><div class="line"><a name="l00045"></a><span class="lineno">   45</span>&#160;    }</div><div class="line"><a name="l00046"></a><span class="lineno">   46</span>&#160;    <span class="keywordflow">else</span> { <span class="comment">/* compound node: put it on top of the queue and decompose it</span></div><div class="line"><a name="l00047"></a><span class="lineno">   47</span>&#160;<span class="comment">              in a later iteration. */</span></div><div class="line"><a name="l00048"></a><span class="lineno">   48</span>&#160;      queue[idx].pos = pos;</div><div class="line"><a name="l00049"></a><span class="lineno">   49</span>&#160;      queue[idx].node = child-1; <span class="comment">// convert index-1 based to index-0 based</span></div><div class="line"><a name="l00050"></a><span class="lineno">   50</span>&#160;      ++idx;</div><div class="line"><a name="l00051"></a><span class="lineno">   51</span>&#160;      pos += node_size[child-1];</div><div class="line"><a name="l00052"></a><span class="lineno">   52</span>&#160;    }</div><div class="line"><a name="l00053"></a><span class="lineno">   53</span>&#160;    <span class="comment">// Second child</span></div><div class="line"><a name="l00054"></a><span class="lineno">   54</span>&#160;    child = merge[parent+N-1];</div><div class="line"><a name="l00055"></a><span class="lineno">   55</span>&#160;    <span class="keywordflow">if</span> (child&lt;0) {</div><div class="line"><a name="l00056"></a><span class="lineno">   56</span>&#160;      order[pos] = -<a class="code" href="cJSON_8cpp.html#ad00efb41ca386db28bacc7aefe79535c">child</a>;</div><div class="line"><a name="l00057"></a><span class="lineno">   57</span>&#160;    }</div><div class="line"><a name="l00058"></a><span class="lineno">   58</span>&#160;    <span class="keywordflow">else</span> {</div><div class="line"><a name="l00059"></a><span class="lineno">   59</span>&#160;      queue[idx].pos = pos;</div><div class="line"><a name="l00060"></a><span class="lineno">   60</span>&#160;      queue[idx].node = child-1;</div><div class="line"><a name="l00061"></a><span class="lineno">   61</span>&#160;      ++idx;</div><div class="line"><a name="l00062"></a><span class="lineno">   62</span>&#160;    }</div><div class="line"><a name="l00063"></a><span class="lineno">   63</span>&#160;  } <span class="keywordflow">while</span> (idx&gt;0);</div><div class="line"><a name="l00064"></a><span class="lineno">   64</span>&#160;}</div><div class="line"><a name="l00065"></a><span class="lineno">   65</span>&#160;</div><div class="line"><a name="l00066"></a><span class="lineno">   66</span>&#160;<span class="preprocessor">#define size_(r_) ( ((r_&lt;N) ? 1 : node_size[r_-N]) )</span></div><div class="line"><a name="l00067"></a><span class="lineno">   67</span>&#160;</div><div class="line"><a name="l00068"></a><span class="lineno">   68</span>&#160;<span class="keyword">template</span> &lt;const <span class="keywordtype">bool</span> sorted&gt;</div><div class="line"><a name="l00069"></a><span class="lineno">   69</span>&#160;<span class="keywordtype">void</span> generate_R_dendrogram(<span class="keywordtype">int</span> * <span class="keyword">const</span> merge, <span class="keywordtype">double</span> * <span class="keyword">const</span> height, <span class="keywordtype">int</span> * <span class="keyword">const</span> order, cluster_result &amp; Z2, <span class="keyword">const</span> <span class="keywordtype">int</span> N) {</div><div class="line"><a name="l00070"></a><span class="lineno">   70</span>&#160;  <span class="comment">// The array &quot;nodes&quot; is a union-find data structure for the cluster</span></div><div class="line"><a name="l00071"></a><span class="lineno">   71</span>&#160;  <span class="comment">// identites (only needed for unsorted cluster_result input).</span></div><div class="line"><a name="l00072"></a><span class="lineno">   72</span>&#160;  union_find <a class="code" href="namespacellvm.html#ad615816ca25b07333f9a7495cbcb8029">nodes</a>(sorted ? 0 : N);</div><div class="line"><a name="l00073"></a><span class="lineno">   73</span>&#160;  <span class="keywordflow">if</span> (!sorted) {</div><div class="line"><a name="l00074"></a><span class="lineno">   74</span>&#160;    std::stable_sort(Z2[0], Z2[N-1]);</div><div class="line"><a name="l00075"></a><span class="lineno">   75</span>&#160;  }</div><div class="line"><a name="l00076"></a><span class="lineno">   76</span>&#160;</div><div class="line"><a name="l00077"></a><span class="lineno">   77</span>&#160;  t_index node1, node2;</div><div class="line"><a name="l00078"></a><span class="lineno">   78</span>&#160;  auto_array_ptr&lt;t_index&gt; node_size(N-1);</div><div class="line"><a name="l00079"></a><span class="lineno">   79</span>&#160;</div><div class="line"><a name="l00080"></a><span class="lineno">   80</span>&#160;  <span class="keywordflow">for</span> (t_index i=0; i&lt;N-1; ++i) {</div><div class="line"><a name="l00081"></a><span class="lineno">   81</span>&#160;    <span class="comment">// Get two data points whose clusters are merged in step i.</span></div><div class="line"><a name="l00082"></a><span class="lineno">   82</span>&#160;    <span class="comment">// Find the cluster identifiers for these points.</span></div><div class="line"><a name="l00083"></a><span class="lineno">   83</span>&#160;    <span class="keywordflow">if</span> (sorted) {</div><div class="line"><a name="l00084"></a><span class="lineno">   84</span>&#160;      node1 = Z2[i]-&gt;node1;</div><div class="line"><a name="l00085"></a><span class="lineno">   85</span>&#160;      node2 = Z2[i]-&gt;node2;</div><div class="line"><a name="l00086"></a><span class="lineno">   86</span>&#160;    }</div><div class="line"><a name="l00087"></a><span class="lineno">   87</span>&#160;    <span class="keywordflow">else</span> {</div><div class="line"><a name="l00088"></a><span class="lineno">   88</span>&#160;      node1 = <a class="code" href="namespacellvm.html#ad615816ca25b07333f9a7495cbcb8029">nodes</a>.Find(Z2[i]-&gt;node1);</div><div class="line"><a name="l00089"></a><span class="lineno">   89</span>&#160;      node2 = <a class="code" href="namespacellvm.html#ad615816ca25b07333f9a7495cbcb8029">nodes</a>.Find(Z2[i]-&gt;node2);</div><div class="line"><a name="l00090"></a><span class="lineno">   90</span>&#160;      <span class="comment">// Merge the nodes in the union-find data structure by making them</span></div><div class="line"><a name="l00091"></a><span class="lineno">   91</span>&#160;      <span class="comment">// children of a new node.</span></div><div class="line"><a name="l00092"></a><span class="lineno">   92</span>&#160;      <a class="code" href="namespacellvm.html#ad615816ca25b07333f9a7495cbcb8029">nodes</a>.Union(node1, node2);</div><div class="line"><a name="l00093"></a><span class="lineno">   93</span>&#160;    }</div><div class="line"><a name="l00094"></a><span class="lineno">   94</span>&#160;    <span class="comment">// Sort the nodes in the output array.</span></div><div class="line"><a name="l00095"></a><span class="lineno">   95</span>&#160;    <span class="keywordflow">if</span> (node1&gt;node2) {</div><div class="line"><a name="l00096"></a><span class="lineno">   96</span>&#160;      t_index tmp = node1;</div><div class="line"><a name="l00097"></a><span class="lineno">   97</span>&#160;      node1 = node2;</div><div class="line"><a name="l00098"></a><span class="lineno">   98</span>&#160;      node2 = tmp;</div><div class="line"><a name="l00099"></a><span class="lineno">   99</span>&#160;    }</div><div class="line"><a name="l00100"></a><span class="lineno">  100</span>&#160;    <span class="comment">/* Conversion between labeling conventions.</span></div><div class="line"><a name="l00101"></a><span class="lineno">  101</span>&#160;<span class="comment">       Input:  singleton nodes 0,...,N-1</span></div><div class="line"><a name="l00102"></a><span class="lineno">  102</span>&#160;<span class="comment">               compound nodes  N,...,2N-2</span></div><div class="line"><a name="l00103"></a><span class="lineno">  103</span>&#160;<span class="comment">       Output: singleton nodes -1,...,-N</span></div><div class="line"><a name="l00104"></a><span class="lineno">  104</span>&#160;<span class="comment">               compound nodes  1,...,N</span></div><div class="line"><a name="l00105"></a><span class="lineno">  105</span>&#160;<span class="comment">    */</span></div><div class="line"><a name="l00106"></a><span class="lineno">  106</span>&#160;    merge[i]     = (node1&lt;N) ? -static_cast&lt;int&gt;(node1)-1</div><div class="line"><a name="l00107"></a><span class="lineno">  107</span>&#160;                              : <span class="keyword">static_cast&lt;</span><span class="keywordtype">int</span><span class="keyword">&gt;</span>(node1)-N+1;</div><div class="line"><a name="l00108"></a><span class="lineno">  108</span>&#160;    merge[i+N-1] = (node2&lt;N) ? -static_cast&lt;int&gt;(node2)-1</div><div class="line"><a name="l00109"></a><span class="lineno">  109</span>&#160;                              : <span class="keyword">static_cast&lt;</span><span class="keywordtype">int</span><span class="keyword">&gt;</span>(node2)-N+1;</div><div class="line"><a name="l00110"></a><span class="lineno">  110</span>&#160;    height[i] = Z2[i]-&gt;dist;</div><div class="line"><a name="l00111"></a><span class="lineno">  111</span>&#160;    node_size[i] = size_(node1) + size_(node2);</div><div class="line"><a name="l00112"></a><span class="lineno">  112</span>&#160;  }</div><div class="line"><a name="l00113"></a><span class="lineno">  113</span>&#160;</div><div class="line"><a name="l00114"></a><span class="lineno">  114</span>&#160;  order_nodes(N, merge, node_size, order);</div><div class="line"><a name="l00115"></a><span class="lineno">  115</span>&#160;}</div><div class="ttc" id="cJSON_8cpp_html_ad00efb41ca386db28bacc7aefe79535c"><div class="ttname"><a href="cJSON_8cpp.html#ad00efb41ca386db28bacc7aefe79535c">child</a></div><div class="ttdeci">cJSON * child</div><div class="ttdef"><b>Definition:</b> <a href="cJSON_8cpp_source.html#l02723">cJSON.cpp:2723</a></div></div>
+<div class="ttc" id="namespacellvm_html_ad615816ca25b07333f9a7495cbcb8029"><div class="ttname"><a href="namespacellvm.html#ad615816ca25b07333f9a7495cbcb8029">llvm::nodes</a></div><div class="ttdeci">iterator_range&lt; typename GraphTraits&lt; GraphType &gt;::nodes_iterator &gt; nodes(const GraphType &amp;G)</div><div class="ttdef"><b>Definition:</b> <a href="GraphTraits_8h_source.html#l00111">GraphTraits.h:111</a></div></div>
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 </li>
 <li>addStoreEdge()
 : <a class="el" href="classSVF_1_1SVFIRBuilder.html#a30f043eeca79259d84b97e265110f018">SVF::SVFIRBuilder</a>
@@ -1037,14 +1040,14 @@ $(function() {
 <li>alias()
 : <a class="el" href="classSVF_1_1BVDataPTAImpl.html#ad3e5b44c21e9d4a38476f39351e56cc9">SVF::BVDataPTAImpl</a>
 , <a class="el" href="classSVF_1_1CFLAlias.html#ab40891c44b83103fc240c1e7c7c60855">SVF::CFLAlias</a>
-, <a class="el" href="classSVF_1_1CondPTAImpl.html#adb1ed3728d53a13c94402392155e9913">SVF::CondPTAImpl&lt; Cond &gt;</a>
-, <a class="el" href="classSVF_1_1DDAPass.html#a96de481dd2af7b39428aff38158c1d4e">SVF::DDAPass</a>
+, <a class="el" href="classSVF_1_1CondPTAImpl.html#ac18e1dc9c6fc8cc952f67a93c2491876">SVF::CondPTAImpl&lt; Cond &gt;</a>
+, <a class="el" href="classSVF_1_1DDAPass.html#a2635769ff8a1e0013b9b8546b18fcfeb">SVF::DDAPass</a>
 , <a class="el" href="classSVF_1_1LockAnalysis.html#a4424f27444c12dce8071c56a95c664bf">SVF::LockAnalysis</a>
-, <a class="el" href="classSVF_1_1PointerAnalysis.html#ae1323233941cdc9b99332e4b954a2217">SVF::PointerAnalysis</a>
+, <a class="el" href="classSVF_1_1PointerAnalysis.html#a0f712ead1f31750879948c36b2fc77cf">SVF::PointerAnalysis</a>
 , <a class="el" href="classSVF_1_1WPAPass.html#a92e19b9ddf342d688ff0f1aa6cecc729">SVF::WPAPass</a>
 </li>
 <li>alias_begin()
-: <a class="el" href="classSVF_1_1SVFModule.html#a0e28f6eaf32efc6f2c0987e64f1df852">SVF::SVFModule</a>
+: <a class="el" href="classSVF_1_1SVFModule.html#a7f2b4647c8d69c8328b63e576cb6d065">SVF::SVFModule</a>
 </li>
 <li>alias_end()
 : <a class="el" href="classSVF_1_1SVFModule.html#a3cfd0983849950099d1e8f8e0fda42bc">SVF::SVFModule</a>
@@ -1155,7 +1158,7 @@ $(function() {
 , <a class="el" href="classSVF_1_1LockAnalysis.html#ad1516b6cb1dbd06b8dff04ae3c944621">SVF::LockAnalysis</a>
 , <a class="el" href="classSVF_1_1LockResultValidator.html#a88ff3ed1398a0b847d71a4c0352ed66d">SVF::LockResultValidator</a>
 , <a class="el" href="classSVF_1_1MHP.html#a02457fa6e3c85c897ec3b3d8db18cc4b">SVF::MHP</a>
-, <a class="el" href="classSVF_1_1MTAResultValidator.html#a13073beef204314602c2dc92ec473484">SVF::MTAResultValidator</a>
+, <a class="el" href="classSVF_1_1MTAResultValidator.html#a462f1554e058b656861abfb0aa2e47ff">SVF::MTAResultValidator</a>
 , <a class="el" href="classSVF_1_1PCG.html#a50b677ec622247a464cee7f0f45c5a53">SVF::PCG</a>
 , <a class="el" href="classSVF_1_1PointerAnalysis.html#ae1e217dc18be0ce70bee5ad930cb54c6">SVF::PointerAnalysis</a>
 , <a class="el" href="classSVF_1_1RaceResultValidator.html#ab8a261120a7f6520d22a6f5cdf2257e9">SVF::RaceResultValidator</a>

package/SVF-doxygen/html/html/functions_b.html

@@ -162,6 +162,9 @@ $(function() {
 , <a class="el" href="classSVF_1_1PersistentVersionedPTData.html#ad4586331863d67e78c54d919694b58db">SVF::PersistentVersionedPTData&lt; Key, KeySet, Data, DataSet, VersionedKey, VersionedKeySet &gt;</a>
 , <a class="el" href="classSVF_1_1VersionedPTData.html#a9833b47df24ed821a55d5ce9a3917f1f">SVF::VersionedPTData&lt; Key, KeySet, Data, DataSet, VersionedKey, VersionedKeySet &gt;</a>
 </li>
+<li>BaseT
+: <a class="el" href="classllvm_1_1iterator__adaptor__base.html#ac1f22569ffff340b8f178b93513bc0eb">llvm::iterator_adaptor_base&lt; DerivedT, WrappedIteratorT, IteratorCategoryT, T, DifferenceTypeT, PointerT, ReferenceT &gt;</a>
+</li>
 <li>BaseVersionedPTData
 : <a class="el" href="classSVF_1_1MutableVersionedPTData.html#aa80044e3b4c3ed58117573dfa54d803b">SVF::MutableVersionedPTData&lt; Key, KeySet, Data, DataSet, VersionedKey, VersionedKeySet &gt;</a>
 , <a class="el" href="classSVF_1_1PersistentVersionedPTData.html#ab71b82478d74f1a20ce3de479f2d8d5c">SVF::PersistentVersionedPTData&lt; Key, KeySet, Data, DataSet, VersionedKey, VersionedKeySet &gt;</a>
@@ -218,6 +221,7 @@ $(function() {
 </li>
 <li>begin()
 : <a class="el" href="classllvm_1_1generic__bridge__gep__type__iterator.html#aabd833b8eca182f681462209c9f24f1a">llvm::generic_bridge_gep_type_iterator&lt; ItTy &gt;</a>
+, <a class="el" href="classllvm_1_1iterator__range.html#af5a020bd9dd7bc8487dd53ce443fdd8f">llvm::iterator_range&lt; IteratorT &gt;</a>
 , <a class="el" href="classSVF_1_1CondPointsToSet.html#a3521ec3be48cc03d9d3f562cb088a9ad">SVF::CondPointsToSet&lt; Cond &gt;</a>
 , <a class="el" href="classSVF_1_1CondStdSet.html#adf095111734d81b6ad1908a7f795b038">SVF::CondStdSet&lt; Element &gt;</a>
 , <a class="el" href="classSVF_1_1ContextCond.html#a4ae7e2236708b0d205f393cdce75c8d1">SVF::ContextCond</a>
@@ -229,6 +233,9 @@ $(function() {
 , <a class="el" href="classSVF_1_1SVFFunction.html#a49a6e9c0661135ceda2dd4d84c4b24ae">SVF::SVFFunction</a>
 , <a class="el" href="classSVF_1_1SVFModule.html#a5486697889c6cca4f9f426650defc255">SVF::SVFModule</a>
 </li>
+<li>begin_iterator
+: <a class="el" href="classllvm_1_1iterator__range.html#aeac0e00835772be18abf2daed29f5d1f">llvm::iterator_range&lt; IteratorT &gt;</a>
+</li>
 <li>BestCandidate
 : <a class="el" href="classSVF_1_1NodeIDAllocator_1_1Clusterer.html#a3556bdda6725b72d0ca88364daeae32e">SVF::NodeIDAllocator::Clusterer</a>
 </li>
@@ -253,21 +260,21 @@ $(function() {
 , <a class="el" href="structSVF_1_1SparseBitVectorElement.html#a4b6a06a3a19f2241cec68e09d4feb526">SVF::SparseBitVectorElement&lt; ElementSize &gt;</a>
 </li>
 <li>BITS_PER_ELEMENT
-: <a class="el" href="structSVF_1_1SparseBitVectorElement.html#a88e49a140a08313ab4d664774c4957a2aeb226b2e0dea78fbdbf5b780c3745f6d">SVF::SparseBitVectorElement&lt; ElementSize &gt;</a>
+: <a class="el" href="structSVF_1_1SparseBitVectorElement.html#a2dfc62db92b64481fe56fafaa923dce0aeb226b2e0dea78fbdbf5b780c3745f6d">SVF::SparseBitVectorElement&lt; ElementSize &gt;</a>
 </li>
 <li>BitVector()
-: <a class="el" href="classSVF_1_1BitVector.html#a212871312b985f7d7215dd46ba171990">SVF::BitVector</a>
+: <a class="el" href="classSVF_1_1BitVector.html#a4a5726a380b115e555944059a507eab7">SVF::BitVector</a>
 , <a class="el" href="classSVF_1_1SparseBitVector_1_1SparseBitVectorIterator.html#aba51f4b0022c38b89f9fa519cf25fb3f">SVF::SparseBitVector&lt; ElementSize &gt;::SparseBitVectorIterator</a>
 </li>
 <li>BitWord
 : <a class="el" href="structSVF_1_1SparseBitVectorElement.html#af9014ab5077a2d9c1aed1e9b1460390d">SVF::SparseBitVectorElement&lt; ElementSize &gt;</a>
 </li>
 <li>BITWORD_SIZE
-: <a class="el" href="classSVF_1_1SparseBitVector.html#ae6cdfbedeb260d7fc91d83f7c1523be8a887a4856f51078b02a23348b7331453e">SVF::SparseBitVector&lt; ElementSize &gt;</a>
-, <a class="el" href="structSVF_1_1SparseBitVectorElement.html#a88e49a140a08313ab4d664774c4957a2a3335c07a7225c80110e998246f96d6c4">SVF::SparseBitVectorElement&lt; ElementSize &gt;</a>
+: <a class="el" href="classSVF_1_1SparseBitVector.html#ab0a250ed14fc688ffb38c8f00aca0bd4a887a4856f51078b02a23348b7331453e">SVF::SparseBitVector&lt; ElementSize &gt;</a>
+, <a class="el" href="structSVF_1_1SparseBitVectorElement.html#a2dfc62db92b64481fe56fafaa923dce0a3335c07a7225c80110e998246f96d6c4">SVF::SparseBitVectorElement&lt; ElementSize &gt;</a>
 </li>
 <li>BITWORDS_PER_ELEMENT
-: <a class="el" href="structSVF_1_1SparseBitVectorElement.html#a88e49a140a08313ab4d664774c4957a2a3dde12fdc7052a87d20741d2c31a65a3">SVF::SparseBitVectorElement&lt; ElementSize &gt;</a>
+: <a class="el" href="structSVF_1_1SparseBitVectorElement.html#a2dfc62db92b64481fe56fafaa923dce0a3dde12fdc7052a87d20741d2c31a65a3">SVF::SparseBitVectorElement&lt; ElementSize &gt;</a>
 </li>
 <li>BlackHole
 : <a class="el" href="classSVF_1_1SymbolTableInfo.html#afd2cf6ef6d7f2a583c709a72067be89ba95734ab884566beab5cd3523c250b539">SVF::SymbolTableInfo</a>
@@ -301,10 +308,10 @@ $(function() {
 : <a class="el" href="classSVF_1_1SVFStat.html#a17c8ea68bf1341ab80f71fff76a9ffce">SVF::SVFStat</a>
 </li>
 <li>BranchStmt()
-: <a class="el" href="classSVF_1_1BranchStmt.html#a83244ad7db61a544f7538961081d4fbd">SVF::BranchStmt</a>
+: <a class="el" href="classSVF_1_1BranchStmt.html#a714d118096f0a3d439cfbff10aa455a2">SVF::BranchStmt</a>
 </li>
 <li>BranchVFGNode()
-: <a class="el" href="classSVF_1_1BranchVFGNode.html#adbaa9b14441cb66ad46671d93c09c513">SVF::BranchVFGNode</a>
+: <a class="el" href="classSVF_1_1BranchVFGNode.html#ad1aa629eae4006a68a1e6e8a7621a494">SVF::BranchVFGNode</a>
 </li>
 <li>BreakConstantGEPs()
 : <a class="el" href="classSVF_1_1BreakConstantGEPs.html#a5397ce21e78d09c8d1cdc3f912d53a7f">SVF::BreakConstantGEPs</a>
@@ -323,7 +330,7 @@ $(function() {
 </li>
 <li>build()
 : <a class="el" href="classSVF_1_1CFLGraphBuilder.html#ab0d2bd46dd1c3be10c04f573e9365757">SVF::CFLGraphBuilder</a>
-, <a class="el" href="classSVF_1_1GrammarBuilder.html#a23d03b2cd348d85bda1ee582dded6505">SVF::GrammarBuilder</a>
+, <a class="el" href="classSVF_1_1GrammarBuilder.html#a11bd8225be12650c811ba968cc3935b3">SVF::GrammarBuilder</a>
 , <a class="el" href="classSVF_1_1ICFGBuilder.html#ae66565ee32fff4ef5f0157e867333250">SVF::ICFGBuilder</a>
 , <a class="el" href="classSVF_1_1LLVMLoopAnalysis.html#a17e4805c2db146430c58af35625a388d">SVF::LLVMLoopAnalysis</a>
 , <a class="el" href="classSVF_1_1LLVMModuleSet.html#af8edfe08027020f14b81b44362c6018e">SVF::LLVMModuleSet</a>
@@ -365,7 +372,7 @@ $(function() {
 : <a class="el" href="classSVF_1_1CHGBuilder.html#a87ad835786fb8fed2a24c122fa839c25">SVF::CHGBuilder</a>
 </li>
 <li>buildCHGNodes()
-: <a class="el" href="classSVF_1_1CHGBuilder.html#a648e97899c16a5634fc8369aef8a031f">SVF::CHGBuilder</a>
+: <a class="el" href="classSVF_1_1CHGBuilder.html#abca5a0a010fdb63a3fa8b92ea0dd55e6">SVF::CHGBuilder</a>
 </li>
 <li>buildClassNameToAncestorsDescendantsMap()
 : <a class="el" href="classSVF_1_1CHGBuilder.html#ae7832c277f0ff86f3ae750aac6063adb">SVF::CHGBuilder</a>
@@ -424,7 +431,7 @@ $(function() {
 : <a class="el" href="classSVF_1_1LLVMLoopAnalysis.html#a82b29fc1e138e082d7da6e016a5b7eb8">SVF::LLVMLoopAnalysis</a>
 </li>
 <li>buildSVFModule()
-: <a class="el" href="classSVF_1_1LLVMModuleSet.html#a1f8e769251c89433311eeb6f98d115e9">SVF::LLVMModuleSet</a>
+: <a class="el" href="classSVF_1_1LLVMModuleSet.html#ae919327019b5014f64b754dbdeb07f75">SVF::LLVMModuleSet</a>
 </li>
 <li>buildThreadCallGraph()
 : <a class="el" href="classSVF_1_1ThreadCallGraphBuilder.html#a0f5bf24257858919c10af0e076d87ef7">SVF::ThreadCallGraphBuilder</a>
@@ -435,12 +442,12 @@ $(function() {
 <li>buildVTables()
 : <a class="el" href="classSVF_1_1DCHGraph.html#a1215db390515a30fbc416fb14d2e863f">SVF::DCHGraph</a>
 </li>
-<li>BV
-: <a class="el" href="classSVF_1_1PointsTo.html#a8f757f92ebf0a2ebdb5e6b001606923eafd6e0658d0eb4cdba368fa8e77d4d892">SVF::PointsTo</a>
-</li>
 <li>bv
 : <a class="el" href="classSVF_1_1PointsTo.html#a668be9270539fdfc5dbf3efb9cc17587">SVF::PointsTo</a>
 </li>
+<li>BV
+: <a class="el" href="classSVF_1_1PointsTo.html#a8f757f92ebf0a2ebdb5e6b001606923eafd6e0658d0eb4cdba368fa8e77d4d892">SVF::PointsTo</a>
+</li>
 <li>bv2int
 : <a class="el" href="classSVF_1_1Z3Expr.html#a349068a6c6c45f42ee3fedb0a487c06a">SVF::Z3Expr</a>
 </li>