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3 <title>MayaChemTools:Code:Graph::CyclesDetection.pm</title>
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13 <pre>
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14 <a name="package-Graph::CyclesDetection-"></a> 1 <span class="k">package </span><span class="i">Graph::CyclesDetection</span><span class="sc">;</span>
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15 2 <span class="c">#</span>
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16 3 <span class="c"># $RCSfile: CyclesDetection.pm,v $</span>
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17 4 <span class="c"># $Date: 2015/02/28 20:49:06 $</span>
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18 5 <span class="c"># $Revision: 1.27 $</span>
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19 6 <span class="c">#</span>
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20 7 <span class="c"># Author: Manish Sud <msud@san.rr.com></span>
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21 8 <span class="c">#</span>
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22 9 <span class="c"># Copyright (C) 2015 Manish Sud. All rights reserved.</span>
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23 10 <span class="c">#</span>
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24 11 <span class="c"># This file is part of MayaChemTools.</span>
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25 12 <span class="c">#</span>
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26 13 <span class="c"># MayaChemTools is free software; you can redistribute it and/or modify it under</span>
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27 14 <span class="c"># the terms of the GNU Lesser General Public License as published by the Free</span>
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28 15 <span class="c"># Software Foundation; either version 3 of the License, or (at your option) any</span>
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29 16 <span class="c"># later version.</span>
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30 17 <span class="c">#</span>
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31 18 <span class="c"># MayaChemTools is distributed in the hope that it will be useful, but without</span>
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32 19 <span class="c"># any warranty; without even the implied warranty of merchantability of fitness</span>
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33 20 <span class="c"># for a particular purpose. See the GNU Lesser General Public License for more</span>
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34 21 <span class="c"># details.</span>
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35 22 <span class="c">#</span>
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36 23 <span class="c"># You should have received a copy of the GNU Lesser General Public License</span>
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37 24 <span class="c"># along with MayaChemTools; if not, see <http://www.gnu.org/licenses/> or</span>
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38 25 <span class="c"># write to the Free Software Foundation Inc., 59 Temple Place, Suite 330,</span>
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39 26 <span class="c"># Boston, MA, 02111-1307, USA.</span>
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40 27 <span class="c">#</span>
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41 28
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42 29 <span class="k">use</span> <span class="w">strict</span><span class="sc">;</span>
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43 30 <span class="k">use</span> <span class="w">Carp</span><span class="sc">;</span>
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44 31 <span class="k">use</span> <span class="w">Exporter</span><span class="sc">;</span>
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45 32 <span class="k">use</span> <span class="w">Graph</span><span class="sc">;</span>
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46 33 <span class="k">use</span> <span class="w">Graph::Path</span><span class="sc">;</span>
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47 34 <span class="k">use</span> <span class="w">Graph::PathGraph</span><span class="sc">;</span>
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48 35 <span class="k">use</span> <span class="w">BitVector</span><span class="sc">;</span>
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49 36
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50 37 <span class="k">use</span> <span class="w">vars</span> <span class="q">qw(@ISA @EXPORT @EXPORT_OK %EXPORT_TAGS)</span><span class="sc">;</span>
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51 38
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52 39 <span class="i">@ISA</span> = <span class="q">qw(Exporter)</span><span class="sc">;</span>
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53 40 <span class="i">@EXPORT</span> = <span class="q">qw()</span><span class="sc">;</span>
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54 41 <span class="i">@EXPORT_OK</span> = <span class="q">qw()</span><span class="sc">;</span>
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55 42
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56 43 <span class="i">%EXPORT_TAGS</span> = <span class="s">(</span><span class="w">all</span> <span class="cm">=></span> <span class="s">[</span><span class="i">@EXPORT</span><span class="cm">,</span> <span class="i">@EXPORT_OK</span><span class="s">]</span><span class="s">)</span><span class="sc">;</span>
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57 44
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58 45 <span class="c"># Setup class variables...</span>
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59 46 <span class="k">my</span><span class="s">(</span><span class="i">$ClassName</span><span class="s">)</span><span class="sc">;</span>
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60 47 <span class="i">_InitializeClass</span><span class="s">(</span><span class="s">)</span><span class="sc">;</span>
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61 48
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62 49 <span class="c"># Overload Perl functions...</span>
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63 50 <span class="k">use</span> <span class="w">overload</span> <span class="q">'""'</span> <span class="cm">=></span> <span class="q">'StringifyCyclesDetection'</span><span class="sc">;</span>
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64 51
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65 52 <span class="c"># Class constructor...</span>
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66 <a name="new-"></a> 53 <span class="k">sub </span><span class="m">new</span> <span class="s">{</span>
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67 54 <span class="k">my</span><span class="s">(</span><span class="i">$Class</span><span class="cm">,</span> <span class="i">$Graph</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span>
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68 55
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69 56 <span class="c"># Initialize object...</span>
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70 57 <span class="k">my</span> <span class="i">$This</span> = <span class="s">{</span><span class="s">}</span><span class="sc">;</span>
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71 58 <span class="k">bless</span> <span class="i">$This</span><span class="cm">,</span> <span class="k">ref</span><span class="s">(</span><span class="i">$Class</span><span class="s">)</span> || <span class="i">$Class</span><span class="sc">;</span>
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72 59 <span class="i">$This</span><span class="i">->_InitializeCyclesDetection</span><span class="s">(</span><span class="i">$Graph</span><span class="s">)</span><span class="sc">;</span>
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73 60
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74 61 <span class="k">return</span> <span class="i">$This</span><span class="sc">;</span>
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75 62 <span class="s">}</span>
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76 63
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77 64 <span class="c"># Initialize object data...</span>
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78 <a name="_InitializeCyclesDetection-"></a> 65 <span class="k">sub </span><span class="m">_InitializeCyclesDetection</span> <span class="s">{</span>
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79 66 <span class="k">my</span><span class="s">(</span><span class="i">$This</span><span class="cm">,</span> <span class="i">$Graph</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span>
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80 67
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81 68 <span class="i">$This</span>->{<span class="w">Graph</span>} = <span class="i">$Graph</span><span class="sc">;</span>
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82 69
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83 70 <span class="c"># Cycles list...</span>
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84 71 <span class="i">@</span>{<span class="i">$This</span>->{<span class="w">AllCyclicPaths</span>}} = <span class="s">(</span><span class="s">)</span><span class="sc">;</span>
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85 72
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86 73 <span class="c"># Cyclic paths which are not part of any other cycle...</span>
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87 74 <span class="i">@</span>{<span class="i">$This</span>->{<span class="w">IndependentCyclicPaths</span>}} = <span class="s">(</span><span class="s">)</span><span class="sc">;</span>
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88 75
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89 76 <span class="k">return</span> <span class="i">$This</span><span class="sc">;</span>
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90 77 <span class="s">}</span>
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91 78
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92 79 <span class="c"># Initialize class ...</span>
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93 <a name="_InitializeClass-"></a> 80 <span class="k">sub </span><span class="m">_InitializeClass</span> <span class="s">{</span>
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94 81 <span class="c">#Class name...</span>
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95 82 <span class="i">$ClassName</span> = <span class="w">__PACKAGE__</span><span class="sc">;</span>
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96 83 <span class="s">}</span>
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97 84
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98 85 <span class="c"># Detect all cycles in graph...</span>
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99 86 <span class="c">#</span>
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100 <a name="DetectCycles-"></a> 87 <span class="k">sub </span><span class="m">DetectCycles</span> <span class="s">{</span>
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101 88 <span class="k">my</span><span class="s">(</span><span class="i">$This</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span>
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102 89
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103 90 <span class="k">return</span> <span class="i">$This</span><span class="i">->DetectCyclesUsingCollapsingPathGraphMethodology</span><span class="s">(</span><span class="s">)</span><span class="sc">;</span>
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104 91 <span class="s">}</span>
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105 92
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106 93 <span class="c"># Detect all cycles in the graph using collapsing path graph [Ref 31] methodology...</span>
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107 94 <span class="c">#</span>
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108 95 <span class="c"># Note:</span>
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109 96 <span class="c"># . For topologically complex graphs containing large number of cycles,</span>
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110 97 <span class="c"># CollapseVertexAndCollectCyclicPathsDetectCycles method implemented in</span>
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111 98 <span class="c"># PathGraph can time out in which case no cycles are detected or</span>
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112 99 <span class="c"># assigned.</span>
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113 100 <span class="c">#</span>
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114 <a name="DetectCyclesUsingCollapsingPathGraphMethodology-"></a> 101 <span class="k">sub </span><span class="m">DetectCyclesUsingCollapsingPathGraphMethodology</span> <span class="s">{</span>
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115 102 <span class="k">my</span><span class="s">(</span><span class="i">$This</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span>
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116 103 <span class="k">my</span><span class="s">(</span><span class="i">$PathGraph</span><span class="s">)</span><span class="sc">;</span>
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117 104
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118 105 <span class="c"># Create a path graph...</span>
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119 106 <span class="i">$PathGraph</span> = <span class="i">new</span> <span class="i">Graph::PathGraph</span><span class="s">(</span><span class="i">$This</span>->{<span class="w">Graph</span>}<span class="s">)</span><span class="sc">;</span>
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120 107
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121 108 <span class="c"># For a vertex to be in a cycle, its degree must be >=2. So delete vertices recursively</span>
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122 109 <span class="c"># till all vertices with degree less than 2 have been deleted...</span>
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123 110 <span class="i">$PathGraph</span><span class="i">->DeleteVerticesWithDegreeLessThan</span><span class="s">(</span><span class="n">2</span><span class="s">)</span><span class="sc">;</span>
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124 111
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125 112 <span class="c"># Setup a VertexID and EdgeID to index map usage during retrieval of independent cycles to</span>
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126 113 <span class="c"># avoid going over all vertices in all cylic paths later...</span>
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127 114 <span class="c">#</span>
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128 115 <span class="k">my</span><span class="s">(</span><span class="i">$VertexIDsToIndicesRef</span><span class="cm">,</span> <span class="i">$LargestVertexIndex</span><span class="cm">,</span> <span class="i">$EdgeIDsToIndicesRef</span><span class="cm">,</span> <span class="i">$LargestEdgeIDIndex</span><span class="s">)</span><span class="sc">;</span>
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129 116 <span class="s">(</span><span class="i">$VertexIDsToIndicesRef</span><span class="cm">,</span> <span class="i">$LargestVertexIndex</span><span class="s">)</span> = <span class="i">$This</span><span class="i">->_SetupVertexIDsToIndicesMap</span><span class="s">(</span><span class="i">$PathGraph</span><span class="s">)</span><span class="sc">;</span>
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130 117 <span class="s">(</span><span class="i">$EdgeIDsToIndicesRef</span><span class="cm">,</span> <span class="i">$LargestEdgeIDIndex</span><span class="s">)</span> = <span class="i">$This</span><span class="i">->_SetupEdgeIDsToIndicesMap</span><span class="s">(</span><span class="i">$PathGraph</span><span class="s">)</span><span class="sc">;</span>
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131 118
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132 119 <span class="c"># Recursively collapse vertices with lowest degree...</span>
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133 120 <span class="k">my</span><span class="s">(</span><span class="i">$VertexID</span><span class="cm">,</span> <span class="i">$CycleVertexID</span><span class="s">)</span><span class="sc">;</span>
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134 121 <span class="k">while</span> <span class="s">(</span><span class="i">$VertexID</span> = <span class="i">$PathGraph</span><span class="i">->GetVertexWithSmallestDegree</span><span class="s">(</span><span class="s">)</span><span class="s">)</span> <span class="s">{</span>
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135 122 <span class="k">if</span> <span class="s">(</span>!<span class="i">$PathGraph</span><span class="i">->CollapseVertexAndCollectCyclicPaths</span><span class="s">(</span><span class="i">$VertexID</span><span class="s">)</span><span class="s">)</span> <span class="s">{</span>
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136 123 <span class="c"># Cycles detection didn't finish...</span>
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137 124 <span class="k">return</span> <span class="k">undef</span><span class="sc">;</span>
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138 125 <span class="s">}</span>
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139 126 <span class="s">}</span>
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140 127
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141 128 <span class="c"># Get detected cycles and save 'em sorted by size...</span>
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142 129 <span class="k">push</span> <span class="i">@</span>{<span class="i">$This</span>->{<span class="w">AllCyclicPaths</span>}}<span class="cm">,</span> <span class="k">sort</span> <span class="s">{</span> <span class="i">$a</span><span class="i">->GetLength</span><span class="s">(</span><span class="s">)</span> <=> <span class="i">$b</span><span class="i">->GetLength</span><span class="s">(</span><span class="s">)</span> <span class="s">}</span> <span class="i">$PathGraph</span><span class="i">->GetCyclicPaths</span><span class="s">(</span><span class="s">)</span><span class="sc">;</span>
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143 130
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144 131 <span class="c"># Retrieve independent cyclic paths...</span>
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145 132 <span class="k">return</span> <span class="i">$This</span><span class="i">->_RetrieveIndependentCycles</span><span class="s">(</span><span class="i">$VertexIDsToIndicesRef</span><span class="cm">,</span> <span class="i">$LargestVertexIndex</span><span class="cm">,</span> <span class="i">$EdgeIDsToIndicesRef</span><span class="cm">,</span> <span class="i">$LargestEdgeIDIndex</span><span class="s">)</span><span class="sc">;</span>
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146 133 <span class="s">}</span>
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147 134
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148 135 <span class="c"># Retrieve and save independent cyclic paths...</span>
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149 136 <span class="c">#</span>
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150 137 <span class="c"># Set of independent cycles identified using this method doesn't correspond to basis set of</span>
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151 138 <span class="c"># rings or smallest set of smallest rings (SSSR) [ Refs 29-30 ]; instead, set of cycles identified</span>
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152 139 <span class="c"># as independent cycles simply correspond to cycles which contain no other cycle as their</span>
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153 140 <span class="c"># subcycles and can't be described as linear combination of smaller cycles. And it also happen</span>
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154 141 <span class="c"># to contain all the rings in basis set of rings and SSSR. In other words, it's a superset of basis set</span>
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155 142 <span class="c"># of cycles and SSSR. For example, six four membered cycles are identified for cubane which is one</span>
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156 143 <span class="c"># more than the basis set of cycles.</span>
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157 144 <span class="c">#</span>
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158 <a name="_RetrieveIndependentCycles-"></a> 145 <span class="k">sub </span><span class="m">_RetrieveIndependentCycles</span> <span class="s">{</span>
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159 146 <span class="k">my</span><span class="s">(</span><span class="i">$This</span><span class="cm">,</span> <span class="i">$VertexIDsToIndicesRef</span><span class="cm">,</span> <span class="i">$LargestVertexIndex</span><span class="cm">,</span> <span class="i">$EdgeIDsToIndicesRef</span><span class="cm">,</span> <span class="i">$LargestEdgeIDIndex</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span>
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160 147
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161 148 <span class="c"># Only 1 or 0 cyclic paths...</span>
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162 149 <span class="k">if</span> <span class="s">(</span><span class="i">@</span>{<span class="i">$This</span>->{<span class="w">AllCyclicPaths</span>}} <= <span class="n">1</span><span class="s">)</span> <span class="s">{</span>
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163 150 <span class="k">push</span> <span class="i">@</span>{<span class="i">$This</span>->{<span class="w">IndependentCyclicPaths</span>}}<span class="cm">,</span> <span class="i">@</span>{<span class="i">$This</span>->{<span class="w">AllCyclicPaths</span>}}<span class="sc">;</span>
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164 151 <span class="k">return</span> <span class="i">$This</span><span class="sc">;</span>
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165 152 <span class="s">}</span>
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166 153
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167 154 <span class="c"># Setup bit vectors for each cyclic path with size of each bit vector corresponding to</span>
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168 155 <span class="c"># maximum vertex index plus one...</span>
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169 156 <span class="k">my</span><span class="s">(</span><span class="i">$CyclicPath</span><span class="cm">,</span> <span class="i">$BitVector</span><span class="cm">,</span> <span class="i">@BitNums</span><span class="cm">,</span> <span class="i">@CyclicPathBitVectors</span><span class="cm">,</span> <span class="i">@CyclicPathEdgeIDsBitVectors</span><span class="s">)</span><span class="sc">;</span>
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170 157
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171 158 <span class="i">@CyclicPathBitVectors</span> = <span class="s">(</span><span class="s">)</span><span class="sc">;</span> <span class="i">@CyclicPathEdgeIDsBitVectors</span> = <span class="s">(</span><span class="s">)</span><span class="sc">;</span>
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172 159
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173 160 <span class="c"># Set bits corresponding to VertexIDs EdgeIDs using their indices...</span>
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174 161 <span class="k">for</span> <span class="i">$CyclicPath</span> <span class="s">(</span><span class="i">@</span>{<span class="i">$This</span>->{<span class="w">AllCyclicPaths</span>}}<span class="s">)</span> <span class="s">{</span>
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175 162 <span class="i">$BitVector</span> = <span class="i">new</span> <span class="i">BitVector</span><span class="s">(</span><span class="i">$LargestVertexIndex</span><span class="s">)</span><span class="sc">;</span>
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176 163 <span class="i">@BitNums</span> = <span class="k">map</span> <span class="s">{</span> <span class="i">$VertexIDsToIndicesRef</span>->{<span class="i">$_</span>} <span class="s">}</span> <span class="i">$CyclicPath</span><span class="i">->GetVertices</span><span class="s">(</span><span class="s">)</span><span class="sc">;</span>
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177 164 <span class="i">$BitVector</span><span class="i">->SetBits</span><span class="s">(</span><span class="i">@BitNums</span><span class="s">)</span><span class="sc">;</span>
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178 165 <span class="k">push</span> <span class="i">@CyclicPathBitVectors</span><span class="cm">,</span> <span class="i">$BitVector</span><span class="sc">;</span>
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179 166
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180 167 <span class="i">$BitVector</span> = <span class="i">new</span> <span class="i">BitVector</span><span class="s">(</span><span class="i">$LargestEdgeIDIndex</span><span class="s">)</span><span class="sc">;</span>
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181 168 <span class="i">@BitNums</span> = <span class="k">map</span> <span class="s">{</span> <span class="i">$EdgeIDsToIndicesRef</span>->{<span class="i">$_</span>} <span class="s">}</span> <span class="i">$This</span><span class="i">->_GetPathEdgeIDs</span><span class="s">(</span><span class="i">$CyclicPath</span><span class="s">)</span><span class="sc">;</span>
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182 169 <span class="i">$BitVector</span><span class="i">->SetBits</span><span class="s">(</span><span class="i">@BitNums</span><span class="s">)</span><span class="sc">;</span>
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183 170 <span class="k">push</span> <span class="i">@CyclicPathEdgeIDsBitVectors</span><span class="cm">,</span> <span class="i">$BitVector</span><span class="sc">;</span>
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184 171 <span class="s">}</span>
|
|
|
185 172
|
|
|
186 173 <span class="c"># First smallest cyclic path always ends up as an independent cyclic path...</span>
|
|
|
187 174 <span class="k">push</span> <span class="i">@</span>{<span class="i">$This</span>->{<span class="w">IndependentCyclicPaths</span>}}<span class="cm">,</span> <span class="i">$This</span>->{<span class="w">AllCyclicPaths</span>}[<span class="n">0</span>]<span class="sc">;</span>
|
|
|
188 175
|
|
|
189 176 <span class="c"># Retrieve other independent cyclic paths...</span>
|
|
|
190 177 <span class="k">my</span><span class="s">(</span><span class="i">$CurrentIndex</span><span class="cm">,</span> <span class="i">$PreviousIndex</span><span class="cm">,</span> <span class="i">$CurrentCyclicPath</span><span class="cm">,</span> <span class="i">$PreviousCyclicPath</span><span class="cm">,</span> <span class="i">$CurrentPathLength</span><span class="cm">,</span> <span class="i">$PreviousPathLength</span><span class="cm">,</span> <span class="i">$CurrentBitVector</span><span class="cm">,</span> <span class="i">$PreviousBitVector</span><span class="cm">,</span> <span class="i">$CurrentAndPreviousBitVectpor</span><span class="cm">,</span> <span class="i">$AllPreviousSmallerPathsBitVector</span><span class="cm">,</span> <span class="i">$AllPreviousSmallerPathsEdgeIDsBitVector</span><span class="cm">,</span> <span class="i">$CurrentEdgeIDsBitVector</span><span class="cm">,</span> <span class="i">$AndBitVector</span><span class="cm">,</span> <span class="i">%SmallerPathAlreadyAdded</span><span class="cm">,</span> <span class="i">%SkipPath</span><span class="s">)</span><span class="sc">;</span>
|
|
|
191 178
|
|
|
192 179 <span class="i">%SkipPath</span> = <span class="s">(</span><span class="s">)</span><span class="sc">;</span>
|
|
|
193 180 <span class="i">%SmallerPathAlreadyAdded</span> = <span class="s">(</span><span class="s">)</span><span class="sc">;</span>
|
|
|
194 181 <span class="i">$AllPreviousSmallerPathsBitVector</span> = <span class="i">new</span> <span class="i">BitVector</span><span class="s">(</span><span class="i">$LargestVertexIndex</span><span class="s">)</span><span class="sc">;</span>
|
|
|
195 182 <span class="i">$AllPreviousSmallerPathsEdgeIDsBitVector</span> = <span class="i">new</span> <span class="i">BitVector</span><span class="s">(</span><span class="i">$LargestEdgeIDIndex</span><span class="s">)</span><span class="sc">;</span>
|
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196 183
|
|
|
197 184 <span class="j">CURRENT:</span> <span class="k">for</span> <span class="i">$CurrentIndex</span> <span class="s">(</span><span class="n">1</span> .. <span class="i">$#</span>{<span class="i">$This</span>->{<span class="w">AllCyclicPaths</span>}}<span class="s">)</span> <span class="s">{</span>
|
|
|
198 185 <span class="k">if</span> <span class="s">(</span><span class="k">exists</span> <span class="i">$SkipPath</span>{<span class="i">$CurrentIndex</span>}<span class="s">)</span> <span class="s">{</span>
|
|
|
199 186 <span class="k">next</span> <span class="j">CURRENT</span><span class="sc">;</span>
|
|
|
200 187 <span class="s">}</span>
|
|
|
201 188 <span class="i">$CurrentCyclicPath</span> = <span class="i">$This</span>->{<span class="w">AllCyclicPaths</span>}[<span class="i">$CurrentIndex</span>]<span class="sc">;</span>
|
|
|
202 189 <span class="i">$CurrentBitVector</span> = <span class="i">$CyclicPathBitVectors</span>[<span class="i">$CurrentIndex</span>]<span class="sc">;</span>
|
|
|
203 190 <span class="i">$CurrentPathLength</span> = <span class="i">$CurrentCyclicPath</span><span class="i">->GetLength</span><span class="s">(</span><span class="s">)</span><span class="sc">;</span>
|
|
|
204 191
|
|
|
205 192 <span class="j">PREVIOUS:</span> <span class="k">for</span> <span class="i">$PreviousIndex</span> <span class="s">(</span><span class="n">0</span> .. <span class="s">(</span><span class="i">$CurrentIndex</span> - <span class="n">1</span><span class="s">)</span><span class="s">)</span> <span class="s">{</span>
|
|
|
206 193 <span class="k">if</span> <span class="s">(</span><span class="k">exists</span> <span class="i">$SkipPath</span>{<span class="i">$PreviousIndex</span>}<span class="s">)</span> <span class="s">{</span>
|
|
|
207 194 <span class="k">next</span> <span class="j">PREVIOUS</span><span class="sc">;</span>
|
|
|
208 195 <span class="s">}</span>
|
|
|
209 196 <span class="i">$PreviousCyclicPath</span> = <span class="i">$This</span>->{<span class="w">AllCyclicPaths</span>}[<span class="i">$PreviousIndex</span>]<span class="sc">;</span>
|
|
|
210 197 <span class="i">$PreviousBitVector</span> = <span class="i">$CyclicPathBitVectors</span>[<span class="i">$PreviousIndex</span>]<span class="sc">;</span>
|
|
|
211 198
|
|
|
212 199 <span class="c"># Is previous path a subset of current path?</span>
|
|
|
213 200 <span class="i">$CurrentAndPreviousBitVectpor</span> = <span class="i">$PreviousBitVector</span> & <span class="i">$CurrentBitVector</span><span class="sc">;</span>
|
|
|
214 201 <span class="k">if</span> <span class="s">(</span><span class="i">$PreviousBitVector</span><span class="i">->GetNumOfSetBits</span><span class="s">(</span><span class="s">)</span> == <span class="i">$CurrentAndPreviousBitVectpor</span><span class="i">->GetNumOfSetBits</span><span class="s">(</span><span class="s">)</span><span class="s">)</span> <span class="s">{</span>
|
|
|
215 202 <span class="c"># Current path doesn't qualify an independent path...</span>
|
|
|
216 203 <span class="i">$SkipPath</span>{<span class="i">$CurrentIndex</span>} = <span class="n">1</span><span class="sc">;</span>
|
|
|
217 204 <span class="k">next</span> <span class="j">CURRENT</span><span class="sc">;</span>
|
|
|
218 205 <span class="s">}</span>
|
|
|
219 206
|
|
|
220 207 <span class="i">$PreviousPathLength</span> = <span class="i">$PreviousCyclicPath</span><span class="i">->GetLength</span><span class="s">(</span><span class="s">)</span><span class="sc">;</span>
|
|
|
221 208 <span class="k">if</span> <span class="s">(</span><span class="i">$PreviousPathLength</span> < <span class="i">$CurrentPathLength</span><span class="s">)</span> <span class="s">{</span>
|
|
|
222 209 <span class="c"># Mark cycle vertices seen in cyclic paths with length smaller than current path...</span>
|
|
|
223 210 <span class="k">if</span> <span class="s">(</span>! <span class="k">exists</span> <span class="i">$SmallerPathAlreadyAdded</span>{<span class="i">$PreviousIndex</span>}<span class="s">)</span> <span class="s">{</span>
|
|
|
224 211 <span class="i">$SmallerPathAlreadyAdded</span>{<span class="i">$PreviousIndex</span>} = <span class="n">1</span><span class="sc">;</span>
|
|
|
225 212 <span class="i">$AllPreviousSmallerPathsBitVector</span> = <span class="i">$AllPreviousSmallerPathsBitVector</span> | <span class="i">$PreviousBitVector</span><span class="sc">;</span>
|
|
|
226 213 <span class="i">$AllPreviousSmallerPathsEdgeIDsBitVector</span> = <span class="i">$AllPreviousSmallerPathsEdgeIDsBitVector</span> | <span class="i">$CyclicPathEdgeIDsBitVectors</span>[<span class="i">$PreviousIndex</span>]<span class="sc">;</span>
|
|
|
227 214 <span class="s">}</span>
|
|
|
228 215 <span class="s">}</span>
|
|
|
229 216 <span class="s">}</span>
|
|
|
230 217 <span class="k">if</span> <span class="s">(</span><span class="i">$AllPreviousSmallerPathsBitVector</span><span class="i">->GetNumOfSetBits</span><span class="s">(</span><span class="s">)</span><span class="s">)</span> <span class="s">{</span>
|
|
|
231 218 <span class="c"># Is current path a linear combination of smaller paths?</span>
|
|
|
232 219 <span class="i">$AndBitVector</span> = <span class="i">$AllPreviousSmallerPathsBitVector</span> & <span class="i">$CurrentBitVector</span><span class="sc">;</span>
|
|
|
233 220 <span class="k">if</span> <span class="s">(</span><span class="i">$CurrentBitVector</span><span class="i">->GetNumOfSetBits</span><span class="s">(</span><span class="s">)</span> == <span class="i">$AndBitVector</span><span class="i">->GetNumOfSetBits</span><span class="s">(</span><span class="s">)</span><span class="s">)</span> <span class="s">{</span>
|
|
|
234 221 <span class="c"># Are all edges in the current path already present in smaller paths?</span>
|
|
|
235 222 <span class="i">$CurrentEdgeIDsBitVector</span> = <span class="i">$CyclicPathEdgeIDsBitVectors</span>[<span class="i">$CurrentIndex</span>]<span class="sc">;</span>
|
|
|
236 223 <span class="i">$AndBitVector</span> = <span class="i">$AllPreviousSmallerPathsEdgeIDsBitVector</span> & <span class="i">$CurrentEdgeIDsBitVector</span><span class="sc">;</span>
|
|
|
237 224
|
|
|
238 225 <span class="k">if</span> <span class="s">(</span><span class="i">$CurrentEdgeIDsBitVector</span><span class="i">->GetNumOfSetBits</span><span class="s">(</span><span class="s">)</span> == <span class="i">$AndBitVector</span><span class="i">->GetNumOfSetBits</span><span class="s">(</span><span class="s">)</span><span class="s">)</span> <span class="s">{</span>
|
|
|
239 226 <span class="c"># Current path doesn't qualify an independent path...</span>
|
|
|
240 227 <span class="i">$SkipPath</span>{<span class="i">$CurrentIndex</span>} = <span class="n">1</span><span class="sc">;</span>
|
|
|
241 228 <span class="k">next</span> <span class="j">CURRENT</span><span class="sc">;</span>
|
|
|
242 229 <span class="s">}</span>
|
|
|
243 230 <span class="s">}</span>
|
|
|
244 231 <span class="s">}</span>
|
|
|
245 232 <span class="c"># It's an independent cyclic path...</span>
|
|
|
246 233 <span class="k">push</span> <span class="i">@</span>{<span class="i">$This</span>->{<span class="w">IndependentCyclicPaths</span>}}<span class="cm">,</span> <span class="i">$CurrentCyclicPath</span><span class="sc">;</span>
|
|
|
247 234 <span class="s">}</span>
|
|
|
248 235 <span class="k">return</span> <span class="i">$This</span><span class="sc">;</span>
|
|
|
249 236 <span class="s">}</span>
|
|
|
250 237
|
|
|
251 238 <span class="c"># Setup a VertexID to index map...</span>
|
|
|
252 239 <span class="c">#</span>
|
|
|
253 <a name="_SetupVertexIDsToIndicesMap-"></a> 240 <span class="k">sub </span><span class="m">_SetupVertexIDsToIndicesMap</span> <span class="s">{</span>
|
|
|
254 241 <span class="k">my</span><span class="s">(</span><span class="i">$This</span><span class="cm">,</span> <span class="i">$PathGraph</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span>
|
|
|
255 242 <span class="k">my</span><span class="s">(</span><span class="i">$LargestVertexIndex</span><span class="cm">,</span> <span class="i">@VertexIDs</span><span class="cm">,</span> <span class="i">%VertexIDsMap</span><span class="s">)</span><span class="sc">;</span>
|
|
|
256 243
|
|
|
257 244 <span class="i">%VertexIDsMap</span> = <span class="s">(</span><span class="s">)</span><span class="sc">;</span> <span class="i">@VertexIDs</span> = <span class="s">(</span><span class="s">)</span><span class="sc">;</span> <span class="i">$LargestVertexIndex</span> = <span class="n">0</span><span class="sc">;</span>
|
|
|
258 245
|
|
|
259 246 <span class="i">@VertexIDs</span> = <span class="i">$PathGraph</span><span class="i">->GetVertices</span><span class="s">(</span><span class="s">)</span><span class="sc">;</span>
|
|
|
260 247 <span class="k">if</span> <span class="s">(</span>! <span class="i">@VertexIDs</span><span class="s">)</span> <span class="s">{</span>
|
|
|
261 248 <span class="k">return</span> <span class="s">(</span>\<span class="i">%VertexIDsMap</span><span class="cm">,</span> <span class="i">$LargestVertexIndex</span><span class="s">)</span><span class="sc">;</span>
|
|
|
262 249 <span class="s">}</span>
|
|
|
263 250 <span class="i">@VertexIDsMap</span>{ <span class="i">@VertexIDs</span> } = <span class="s">(</span><span class="n">0</span> .. <span class="i">$#VertexIDs</span><span class="s">)</span><span class="sc">;</span>
|
|
|
264 251 <span class="i">$LargestVertexIndex</span> = <span class="k">scalar</span> <span class="i">@VertexIDs</span><span class="sc">;</span>
|
|
|
265 252
|
|
|
266 253 <span class="k">return</span> <span class="s">(</span>\<span class="i">%VertexIDsMap</span><span class="cm">,</span> <span class="i">$LargestVertexIndex</span><span class="s">)</span><span class="sc">;</span>
|
|
|
267 254 <span class="s">}</span>
|
|
|
268 255
|
|
|
269 256 <span class="c"># Setup a Edge to index map using paths associated to egdes in an intial</span>
|
|
|
270 257 <span class="c"># path graph...</span>
|
|
|
271 258 <span class="c">#</span>
|
|
|
272 <a name="_SetupEdgeIDsToIndicesMap-"></a> 259 <span class="k">sub </span><span class="m">_SetupEdgeIDsToIndicesMap</span> <span class="s">{</span>
|
|
|
273 260 <span class="k">my</span><span class="s">(</span><span class="i">$This</span><span class="cm">,</span> <span class="i">$PathGraph</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span>
|
|
|
274 261 <span class="k">my</span><span class="s">(</span><span class="i">$Path</span><span class="cm">,</span> <span class="i">$LargestEdgeIndex</span><span class="cm">,</span> <span class="i">@EdgeIDs</span><span class="cm">,</span> <span class="i">%EdgeIDsMap</span><span class="s">)</span><span class="sc">;</span>
|
|
|
275 262
|
|
|
276 263 <span class="i">%EdgeIDsMap</span> = <span class="s">(</span><span class="s">)</span><span class="sc">;</span> <span class="i">@EdgeIDs</span> = <span class="s">(</span><span class="s">)</span><span class="sc">;</span> <span class="i">$LargestEdgeIndex</span> = <span class="n">0</span><span class="sc">;</span>
|
|
|
277 264
|
|
|
278 265 <span class="i">@EdgeIDs</span> = <span class="s">(</span><span class="s">)</span><span class="sc">;</span>
|
|
|
279 266 <span class="k">for</span> <span class="i">$Path</span> <span class="s">(</span><span class="i">$PathGraph</span><span class="i">->GetPaths</span><span class="s">(</span><span class="s">)</span><span class="s">)</span> <span class="s">{</span>
|
|
|
280 267 <span class="k">push</span> <span class="i">@EdgeIDs</span><span class="cm">,</span> <span class="i">$This</span><span class="i">->_GetPathEdgeIDs</span><span class="s">(</span><span class="i">$Path</span><span class="s">)</span><span class="sc">;</span>
|
|
|
281 268 <span class="s">}</span>
|
|
|
282 269
|
|
|
283 270 <span class="k">if</span> <span class="s">(</span>! <span class="i">@EdgeIDs</span><span class="s">)</span> <span class="s">{</span>
|
|
|
284 271 <span class="k">return</span> <span class="s">(</span>\<span class="i">%EdgeIDsMap</span><span class="cm">,</span> <span class="i">$LargestEdgeIndex</span><span class="s">)</span><span class="sc">;</span>
|
|
|
285 272 <span class="s">}</span>
|
|
|
286 273
|
|
|
287 274 <span class="i">@EdgeIDsMap</span>{ <span class="i">@EdgeIDs</span> } = <span class="s">(</span><span class="n">0</span> .. <span class="i">$#EdgeIDs</span><span class="s">)</span><span class="sc">;</span>
|
|
|
288 275 <span class="i">$LargestEdgeIndex</span> = <span class="k">scalar</span> <span class="i">@EdgeIDs</span><span class="sc">;</span>
|
|
|
289 276
|
|
|
290 277 <span class="k">return</span> <span class="s">(</span>\<span class="i">%EdgeIDsMap</span><span class="cm">,</span> <span class="i">$LargestEdgeIndex</span><span class="s">)</span><span class="sc">;</span>
|
|
|
291 278 <span class="s">}</span>
|
|
|
292 279
|
|
|
293 280 <span class="c"># Get path edge IDs or number of edges. The edge IDs are generated from</span>
|
|
|
294 281 <span class="c"># edge vertices and correpond to VertexID1-VertexID2 where VertexID1 <=</span>
|
|
|
295 282 <span class="c"># VertexID2.</span>
|
|
|
296 283 <span class="c">#</span>
|
|
|
297 <a name="_GetPathEdgeIDs-"></a> 284 <span class="k">sub </span><span class="m">_GetPathEdgeIDs</span> <span class="s">{</span>
|
|
|
298 285 <span class="k">my</span><span class="s">(</span><span class="i">$This</span><span class="cm">,</span> <span class="i">$Path</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span>
|
|
|
299 286 <span class="k">my</span><span class="s">(</span><span class="i">@EdgesVertexIDs</span><span class="cm">,</span> <span class="i">@EdgeIDs</span><span class="s">)</span><span class="sc">;</span>
|
|
|
300 287
|
|
|
301 288 <span class="i">@EdgesVertexIDs</span> = <span class="s">(</span><span class="s">)</span><span class="sc">;</span> <span class="i">@EdgeIDs</span> = <span class="s">(</span><span class="s">)</span><span class="sc">;</span>
|
|
|
302 289 <span class="i">@EdgesVertexIDs</span> = <span class="i">$Path</span><span class="i">->GetEdges</span><span class="s">(</span><span class="s">)</span><span class="sc">;</span>
|
|
|
303 290 <span class="k">if</span> <span class="s">(</span>!<span class="i">@EdgesVertexIDs</span><span class="s">)</span> <span class="s">{</span>
|
|
|
304 291 <span class="k">return</span> <span class="k">wantarray</span> ? <span class="i">@EdgeIDs</span> <span class="co">:</span> <span class="s">(</span><span class="k">scalar</span> <span class="i">@EdgeIDs</span><span class="s">)</span><span class="sc">;</span>
|
|
|
305 292 <span class="s">}</span>
|
|
|
306 293
|
|
|
307 294 <span class="c"># Set up edge IDs...</span>
|
|
|
308 295 <span class="k">my</span><span class="s">(</span><span class="i">$Index</span><span class="cm">,</span> <span class="i">$VertexID1</span><span class="cm">,</span> <span class="i">$VertexID2</span><span class="cm">,</span> <span class="i">$EdgeID</span><span class="s">)</span><span class="sc">;</span>
|
|
|
309 296
|
|
|
310 297 <span class="k">for</span> <span class="s">(</span><span class="i">$Index</span> = <span class="n">0</span><span class="sc">;</span> <span class="i">$Index</span> < <span class="i">$#EdgesVertexIDs</span><span class="sc">;</span> <span class="i">$Index</span> += <span class="n">2</span><span class="s">)</span> <span class="s">{</span>
|
|
|
311 298 <span class="i">$VertexID1</span> = <span class="i">$EdgesVertexIDs</span>[<span class="i">$Index</span>]<span class="sc">;</span> <span class="i">$VertexID2</span> = <span class="i">$EdgesVertexIDs</span>[<span class="i">$Index</span> + <span class="n">1</span>]<span class="sc">;</span>
|
|
|
312 299 <span class="i">$EdgeID</span> = <span class="s">(</span><span class="i">$VertexID1</span> <= <span class="i">$VertexID2</span><span class="s">)</span> ? <span class="q">"$VertexID1-$VertexID2"</span> <span class="co">:</span> <span class="q">"$VertexID2-$VertexID1"</span><span class="sc">;</span>
|
|
|
313 300 <span class="k">push</span> <span class="i">@EdgeIDs</span><span class="cm">,</span> <span class="i">$EdgeID</span><span class="sc">;</span>
|
|
|
314 301 <span class="s">}</span>
|
|
|
315 302
|
|
|
316 303 <span class="k">return</span> <span class="k">wantarray</span> ? <span class="i">@EdgeIDs</span> <span class="co">:</span> <span class="s">(</span><span class="k">scalar</span> <span class="i">@EdgeIDs</span><span class="s">)</span><span class="sc">;</span>
|
|
|
317 304 <span class="s">}</span>
|
|
|
318 305
|
|
|
319 306 <span class="c"># Return an array containing references to cyclic paths or number of cylic paths...</span>
|
|
|
320 307 <span class="c">#</span>
|
|
|
321 <a name="GetAllCyclicPaths-"></a> 308 <span class="k">sub </span><span class="m">GetAllCyclicPaths</span> <span class="s">{</span>
|
|
|
322 309 <span class="k">my</span><span class="s">(</span><span class="i">$This</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span>
|
|
|
323 310
|
|
|
324 311 <span class="k">return</span> <span class="k">wantarray</span> ? <span class="i">@</span>{<span class="i">$This</span>->{<span class="w">AllCyclicPaths</span>}} <span class="co">:</span> <span class="k">scalar</span> <span class="i">@</span>{<span class="i">$This</span>->{<span class="w">AllCyclicPaths</span>}}<span class="sc">;</span>
|
|
|
325 312 <span class="s">}</span>
|
|
|
326 313
|
|
|
327 314 <span class="c"># Get cyclic paths which are independent. In otherwords, cycles which don't contain any other</span>
|
|
|
328 315 <span class="c"># cycle as their subset...</span>
|
|
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329 316 <span class="c">#</span>
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330 <a name="GetIndependentCyclicPaths-"></a> 317 <span class="k">sub </span><span class="m">GetIndependentCyclicPaths</span> <span class="s">{</span>
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331 318 <span class="k">my</span><span class="s">(</span><span class="i">$This</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span>
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332 319
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333 320 <span class="k">return</span> <span class="k">wantarray</span> ? <span class="i">@</span>{<span class="i">$This</span>->{<span class="w">IndependentCyclicPaths</span>}} <span class="co">:</span> <span class="k">scalar</span> <span class="i">@</span>{<span class="i">$This</span>->{<span class="w">IndependentCyclicPaths</span>}}<span class="sc">;</span>
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334 321 <span class="s">}</span>
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335 322
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336 323 <span class="c"># Return a string containg data for CyclesDetection object...</span>
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337 <a name="StringifyCyclesDetection-"></a> 324 <span class="k">sub </span><span class="m">StringifyCyclesDetection</span> <span class="s">{</span>
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338 325 <span class="k">my</span><span class="s">(</span><span class="i">$This</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span>
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339 326 <span class="k">my</span><span class="s">(</span><span class="i">$CyclesDetectionString</span><span class="cm">,</span> <span class="i">$CyclesCount</span><span class="cm">,</span> <span class="i">$CyclicPath</span><span class="s">)</span><span class="sc">;</span>
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340 327
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341 328 <span class="i">$CyclesCount</span> = <span class="i">@</span>{<span class="i">$This</span>->{<span class="w">AllCyclicPaths</span>}}<span class="sc">;</span>
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342 329 <span class="i">$CyclesDetectionString</span> = <span class="q">"AllCycles: Count - $CyclesCount"</span><span class="sc">;</span>
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343 330 <span class="k">for</span> <span class="i">$CyclicPath</span> <span class="s">(</span><span class="i">@</span>{<span class="i">$This</span>->{<span class="w">AllCyclicPaths</span>}}<span class="s">)</span> <span class="s">{</span>
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344 331 <span class="i">$CyclesDetectionString</span> .= <span class="q">"; Cycle: "</span> . <span class="k">join</span><span class="s">(</span><span class="q">'-'</span><span class="cm">,</span> <span class="i">$CyclicPath</span><span class="i">->GetVertices</span><span class="s">(</span><span class="s">)</span><span class="s">)</span><span class="sc">;</span>
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345 332 <span class="s">}</span>
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346 333
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347 334 <span class="i">$CyclesCount</span> = <span class="i">@</span>{<span class="i">$This</span>->{<span class="w">IndependentCyclicPaths</span>}}<span class="sc">;</span>
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348 335 <span class="i">$CyclesDetectionString</span> .= <span class="q">"\nIndependentCycles: Count - $CyclesCount"</span><span class="sc">;</span>
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349 336 <span class="k">for</span> <span class="i">$CyclicPath</span> <span class="s">(</span><span class="i">@</span>{<span class="i">$This</span>->{<span class="w">IndependentCyclicPaths</span>}}<span class="s">)</span> <span class="s">{</span>
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350 337 <span class="i">$CyclesDetectionString</span> .= <span class="q">"; Cycle: "</span> . <span class="k">join</span><span class="s">(</span><span class="q">'-'</span><span class="cm">,</span> <span class="i">$CyclicPath</span><span class="i">->GetVertices</span><span class="s">(</span><span class="s">)</span><span class="s">)</span><span class="sc">;</span>
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351 338 <span class="s">}</span>
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352 339
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353 340 <span class="k">return</span> <span class="i">$CyclesDetectionString</span><span class="sc">;</span>
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354 341 <span class="s">}</span>
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355 342
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356 343 <span class="c"># Return a reference to new cycle detection object...</span>
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357 <a name="Copy-"></a> 344 <span class="k">sub </span><span class="m">Copy</span> <span class="s">{</span>
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358 345 <span class="k">my</span><span class="s">(</span><span class="i">$This</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span>
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359 346 <span class="k">my</span><span class="s">(</span><span class="i">$NewCyclesDetection</span><span class="s">)</span><span class="sc">;</span>
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360 347
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361 348 <span class="i">$NewCyclesDetection</span> = <span class="i">Storable::dclone</span><span class="s">(</span><span class="i">$This</span><span class="s">)</span><span class="sc">;</span>
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362 349
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363 350 <span class="k">return</span> <span class="i">$NewCyclesDetection</span><span class="sc">;</span>
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364 351 <span class="s">}</span>
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365 352
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366 <a name="EOF-"></a></pre>
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367 <p> </p>
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368 <br />
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369 <center>
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370 <img src="../../../images/h2o2.png">
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371 </center>
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372 </body>
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373 </html>
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